| Year |
Citation |
Score |
| 2025 |
Khmelinskaia A, Bethel NP, Fatehi F, Mallik BB, Antanasijevic A, Borst AJ, Lai SH, Chim HY, Wang JY', Miranda MC, Watkins AM, Ogohara C, Caldwell S, Wu M, Heck AJR, ... ... Baker D, et al. Local structural flexibility drives oligomorphism in computationally designed protein assemblies. Nature Structural & Molecular Biology. PMID 40011747 DOI: 10.1038/s41594-025-01490-z |
0.778 |
|
| 2025 |
Yang W, Hicks DR, Ghosh A, Schwartze TA, Conventry B, Goreshnik I, Allen A, Halabiya SF, Kim CJ, Hinck CS, Lee DS, Bera AK, Li Z, Wang Y, Schlichthaerle T, ... ... Baker D, et al. Design of high-affinity binders to immune modulating receptors for cancer immunotherapy. Nature Communications. 16: 2001. PMID 40011465 DOI: 10.1038/s41467-025-57192-z |
0.444 |
|
| 2024 |
Liu Y, Weidle C, Mihaljević L, Watson JL, Li Z, Yu LT, Majumder S, Borst AJ, Carr KD, Kibler RD, Gamal El-Din TM, Catterall WA, Baker D. Bottom-up design of calcium channels from defined selectivity filter geometry. Biorxiv : the Preprint Server For Biology. PMID 39763961 DOI: 10.1101/2024.12.19.629320 |
0.308 |
|
| 2024 |
Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Carr A, Li X, Chow CM, Nguyen TK, Carter L, Wysocki VH, Stoddard BL, Baker D. Design of pseudosymmetric protein hetero-oligomers. Nature Communications. 15: 10684. PMID 39695145 DOI: 10.1038/s41467-024-54913-8 |
0.334 |
|
| 2024 |
Glögl M, Krishnakumar A, Ragotte RJ, Goreshnik I, Coventry B, Bera AK, Kang A, Joyce E, Ahn G, Huang B, Yang W, Chen W, Sanchez MG, Koepnick B, Baker D. Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists. Science (New York, N.Y.). 386: 1154-1161. PMID 39636970 DOI: 10.1126/science.adp1779 |
0.357 |
|
| 2024 |
Rettie SA, Juergens D, Adebomi V, Bueso YF, Zhao Q, Leveille AN, Liu A, Bera AK, Wilms JA, Üffing A, Kang A, Brackenbrough E, Lamb M, Gerben SR, Murray A, ... ... Baker D, et al. Accurate design of high-affinity protein binding macrocycles using deep learning. Biorxiv : the Preprint Server For Biology. PMID 39605685 DOI: 10.1101/2024.11.18.622547 |
0.817 |
|
| 2024 |
Wang S, Favor A, Kibler RD, Lubner JM, Borst AJ, Coudray N, Redler R, Chiang HT, Sheffler W, Hsia Y, Li Z, Ekiert DC, Bhabha G, Pozzo LD, Baker D. Bond-centric modular design of protein assemblies. Biorxiv : the Preprint Server For Biology. PMID 39416012 DOI: 10.1101/2024.10.11.617872 |
0.741 |
|
| 2024 |
Lisanza SL, Gershon JM, Tipps SWK, Sims JN, Arnoldt L, Hendel SJ, Simma MK, Liu G, Yase M, Wu H, Tharp CD, Li X, Kang A, Brackenbrough E, Bera AK, ... ... Baker D, et al. Publisher Correction: Multistate and functional protein design using RoseTTAFold sequence space diffusion. Nature Biotechnology. PMID 39375454 DOI: 10.1038/s41587-024-02456-0 |
0.684 |
|
| 2024 |
Shen H, Lynch EM, Watson JL, Wu K, Bai H, Sheffler W, Derivery E, Kollman J, Baker D. Nucleation limited assembly and polarized growth of a -designed allosterically modulatable protein filament. Biorxiv : the Preprint Server For Biology. PMID 39345553 DOI: 10.1101/2024.09.20.613980 |
0.797 |
|
| 2024 |
Lisanza SL, Gershon JM, Tipps SWK, Sims JN, Arnoldt L, Hendel SJ, Simma MK, Liu G, Yase M, Wu H, Tharp CD, Li X, Kang A, Brackenbrough E, Bera AK, ... ... Baker D, et al. Multistate and functional protein design using RoseTTAFold sequence space diffusion. Nature Biotechnology. PMID 39322764 DOI: 10.1038/s41587-024-02395-w |
0.717 |
|
| 2024 |
Moyer AP, Ramelot TA, Curti M, Eastman MA, Kang A, Bera AK, Tejero R, Salveson PJ, Curutchet C, Romero E, Montelione GT, Baker D. Enumerative Discovery of Noncanonical Polypeptide Secondary Structures. Journal of the American Chemical Society. PMID 39231524 DOI: 10.1021/jacs.4c04991 |
0.776 |
|
| 2024 |
Sun K, Li S, Zheng B, Zhu Y, Wang T, Liang M, Yao Y, Zhang K, Zhang J, Li H, Han D, Zheng J, Coventry B, Cao L, Baker D, et al. Accurate de novo design of heterochiral protein-protein interactions. Cell Research. PMID 39143121 DOI: 10.1038/s41422-024-01014-2 |
0.728 |
|
| 2024 |
Wu K, Jiang H, Hicks DR, Liu C, Muratspahić E, Ramelot TA, Liu Y, McNally K, Gaur A, Coventry B, Chen W, Bera AK, Kang A, Gerben S, Lamb MY, ... ... Baker D, et al. Sequence-specific targeting of intrinsically disordered protein regions. Biorxiv : the Preprint Server For Biology. PMID 39071356 DOI: 10.1101/2024.07.15.603480 |
0.38 |
|
| 2024 |
Liu C, Wu K, Choi H, Han H, Zhang X, Watson JL, Shijo S, Bera AK, Kang A, Brackenbrough E, Coventry B, Hick DR, Hoofnagle AN, Zhu P, Li X, ... ... Baker D, et al. Diffusing protein binders to intrinsically disordered proteins. Biorxiv : the Preprint Server For Biology. PMID 39071267 DOI: 10.1101/2024.07.16.603789 |
0.328 |
|
| 2024 |
An L, Said M, Tran L, Majumder S, Goreshnik I, Lee GR, Juergens D, Dauparas J, Anishchenko I, Coventry B, Bera AK, Kang A, Levine PM, Alvarez V, Pillai A, ... ... Baker D, et al. Binding and sensing diverse small molecules using shape-complementary pseudocycles. Science (New York, N.Y.). 385: 276-282. PMID 39024436 DOI: 10.1126/science.adn3780 |
0.771 |
|
| 2024 |
Peruzzi JA, Gunnels TF, Edelstein HI, Lu P, Baker D, Leonard JN, Kamat NP. Enhancing extracellular vesicle cargo loading and functional delivery by engineering protein-lipid interactions. Nature Communications. 15: 5618. PMID 38965227 DOI: 10.1038/s41467-024-49678-z |
0.69 |
|
| 2024 |
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, et al. Computational design of soluble and functional membrane protein analogues. Nature. PMID 38898281 DOI: 10.1038/s41586-024-07601-y |
0.649 |
|
| 2024 |
Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, ... ... Baker D, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell. PMID 38861993 DOI: 10.1016/j.cell.2024.05.025 |
0.393 |
|
| 2024 |
Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, ... ... Baker D, et al. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nature Chemical Biology. PMID 38831036 DOI: 10.1038/s41589-024-01626-0 |
0.784 |
|
| 2024 |
Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks DR, Pyles H, Yang A, Carter L, Lamb M, Li X, Levine PM, Stewart L, Garcia KC, ... Baker D, et al. De novo design of buttressed loops for sculpting protein functions. Nature Chemical Biology. PMID 38816644 DOI: 10.1038/s41589-024-01632-2 |
0.313 |
|
| 2024 |
Baker D, Yang W, Hicks DR, Ghosh A, Schwartze TA, Coventry B, Goreshnik I, Allen A, Halabiya S, Kim C, Hinck CS, Lee DS, Bera A, Li Z, Wang Y, et al. Design of High Affinity Binders to Convex Protein Target Sites. Biorxiv : the Preprint Server For Biology. PMID 38746206 DOI: 10.1101/2024.05.01.592114 |
0.477 |
|
| 2024 |
Salveson PJ, Moyer AP, Said MY, Gӧkçe G, Li X, Kang A, Nguyen H, Bera AK, Levine PM, Bhardwaj G, Baker D. Expansive discovery of chemically diverse structured macrocyclic oligoamides. Science (New York, N.Y.). 384: 420-428. PMID 38662830 DOI: 10.1126/science.adk1687 |
0.786 |
|
| 2024 |
Peruzzi JA, Steinkühler J, Vu TQ, Gunnels TF, Hu VT, Lu P, Baker D, Kamat NP. Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes. Nature Communications. 15: 3162. PMID 38605024 DOI: 10.1038/s41467-024-47163-1 |
0.682 |
|
| 2024 |
Shen H, Lynch EM, Akkineni S, Watson JL, Decarreau J, Bethel NP, Benna I, Sheffler W, Farrell D, DiMaio F, Derivery E, De Yoreo JJ, Kollman J, Baker D. De novo design of pH-responsive self-assembling helical protein filaments. Nature Nanotechnology. PMID 38570702 DOI: 10.1038/s41565-024-01641-1 |
0.797 |
|
| 2024 |
Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, et al. Computational design of soluble functional analogues of integral membrane proteins. Biorxiv : the Preprint Server For Biology. PMID 38496615 DOI: 10.1101/2023.05.09.540044 |
0.645 |
|
| 2024 |
Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Weidle C, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, ... ... Baker D, et al. Blueprinting extendable nanomaterials with standardized protein blocks. Nature. PMID 38480887 DOI: 10.1038/s41586-024-07188-4 |
0.705 |
|
| 2024 |
Baker D, Church G. Protein design meets biosecurity. Science (New York, N.Y.). 383: 349. PMID 38271530 DOI: 10.1126/science.ado1671 |
0.479 |
|
| 2023 |
An L, Said M, Tran L, Majumder S, Goreshnik I, Lee GR, Juergens D, Dauparas J, Anishchenko I, Coventry B, Bera AK, Kang A, Levine PM, Alvarez V, Pillai A, ... ... Baker D, et al. De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles. Biorxiv : the Preprint Server For Biology. PMID 38187589 DOI: 10.1101/2023.12.20.572602 |
0.775 |
|
| 2023 |
Torres SV, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AH, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, ... ... Baker D, et al. De novo design of high-affinity binders of bioactive helical peptides. Nature. PMID 38109936 DOI: 10.1038/s41586-023-06953-1 |
0.755 |
|
| 2023 |
Olshefsky A, Benasutti H, Sylvestre M, Butterfield GL, Rocklin GJ, Richardson C, Hicks DR, Lajoie MJ, Song K, Leaf E, Treichel C, Decarreau J, Ke S, Kher G, Carter L, ... ... Baker D, et al. In vivo selection of synthetic nucleocapsids for tissue targeting. Proceedings of the National Academy of Sciences of the United States of America. 120: e2306129120. PMID 37939083 DOI: 10.1073/pnas.2306129120 |
0.729 |
|
| 2023 |
Khmelinskaia A, Bethel NP, Fatehi F, Antanasijevic A, Borst AJ, Lai SH, Wang JYJ, Mallik BB, Miranda MC, Watkins AM, Ogohara C, Caldwell S, Wu M, Heck AJR, Veesler D, ... ... Baker D, et al. Local structural flexibility drives oligomorphism in computationally designed protein assemblies. Biorxiv : the Preprint Server For Biology. PMID 37905007 DOI: 10.1101/2023.10.18.562842 |
0.783 |
|
| 2023 |
Li Z, Wang S, Nattermann U, Bera AK, Borst AJ, Yaman MY, Bick MJ, Yang EC, Sheffler W, Lee B, Seifert S, Hura GL, Nguyen H, Kang A, Dalal R, ... ... Baker D, et al. Accurate computational design of three-dimensional protein crystals. Nature Materials. PMID 37845322 DOI: 10.1038/s41563-023-01683-1 |
0.74 |
|
| 2023 |
Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E, Iliopoulos I, Konstantinidis K, ... ... Baker D, et al. Unraveling the functional dark matter through global metagenomics. Nature. 622: 594-602. PMID 37821698 DOI: 10.1038/s41586-023-06583-7 |
0.737 |
|
| 2023 |
Huang B, Abedi M, Ahn G, Coventry B, Sappington I, Wang R, Schlichthaerle T, Zhang JZ, Wang Y, Goreshnik I, Chiu CW, Chazin-Gray A, Chan S, Gerben S, Murray A, ... ... Baker D, et al. Designed Endocytosis-Triggering Proteins mediate Targeted Degradation. Biorxiv : the Preprint Server For Biology. PMID 37781607 DOI: 10.1101/2023.08.19.553321 |
0.321 |
|
| 2023 |
An L, Hicks DR, Zorine D, Dauparas J, Wicky BIM, Milles LF, Courbet A, Bera AK, Nguyen H, Kang A, Carter L, Baker D. Hallucination of closed repeat proteins containing central pockets. Nature Structural & Molecular Biology. PMID 37770718 DOI: 10.1038/s41594-023-01112-6 |
0.304 |
|
| 2023 |
Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks D, Pyles H, Yang A, Carter L, Lamb M, Li X, Levine PM, Stewart L, Garcia KC, ... Baker D, et al. design of buttressed loops for sculpting protein functions. Biorxiv : the Preprint Server For Biology. PMID 37662224 DOI: 10.1101/2023.08.22.554384 |
0.316 |
|
| 2023 |
Praetorius F, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, ... ... Baker D, et al. Design of stimulus-responsive two-state hinge proteins. Science (New York, N.Y.). 381: 754-760. PMID 37590357 DOI: 10.1126/science.adg7731 |
0.749 |
|
| 2023 |
Watson JL, Juergens D, Bennett NR, Trippe BL, Yim J, Eisenach HE, Ahern W, Borst AJ, Ragotte RJ, Milles LF, Wicky BIM, Hanikel N, Pellock SJ, Courbet A, Sheffler W, ... ... Baker D, et al. De novo design of protein structure and function with RFdiffusion. Nature. PMID 37433327 DOI: 10.1038/s41586-023-06415-8 |
0.809 |
|
| 2023 |
Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Weidle C, ... ... Baker D, et al. Blueprinting expandable nanomaterials with standardized protein building blocks. Biorxiv : the Preprint Server For Biology. PMID 37333359 DOI: 10.1101/2023.06.09.544258 |
0.703 |
|
| 2023 |
Sheffler W, Yang EC, Dowling Q, Hsia Y, Fries CN, Stanislaw J, Langowski MD, Brandys M, Li Z, Skotheim R, Borst AJ, Khmelinskaia A, King NP, Baker D. Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. Plos Computational Biology. 19: e1010680. PMID 37216343 DOI: 10.1371/journal.pcbi.1010680 |
0.738 |
|
| 2023 |
Ennist N, Wang S, Kennedy M, Curti M, Sutherland G, Vasilev C, Redler R, Maffeis V, Shareef S, Sica A, Hua A, Deshmukh A, Moyer A, Hicks D, Swartz A, ... ... Baker D, et al. De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs. Research Square. PMID 37131790 DOI: 10.21203/rs.3.rs-2736786/v1 |
0.784 |
|
| 2023 |
Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, ... ... Baker D, et al. Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.). 380: 266-273. PMID 37079676 DOI: 10.1126/science.adf6591 |
0.414 |
|
| 2023 |
Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Li X, Chow CM, Carter L, Wysocki VH, Stoddard BL, Baker D. Stepwise design of pseudosymmetric protein hetero-oligomers. Biorxiv : the Preprint Server For Biology. PMID 37066191 DOI: 10.1101/2023.04.07.535760 |
0.31 |
|
| 2023 |
Wu K, Bai H, Chang YT, Redler R, McNally KE, Sheffler W, Brunette TJ, Hicks DR, Morgan TE, Stevens TJ, Broerman A, Goreshnik I, DeWitt M, Chow CM, Shen Y, ... ... Baker D, et al. De novo design of modular peptide-binding proteins by superhelical matching. Nature. PMID 37020023 DOI: 10.1038/s41586-023-05909-9 |
0.698 |
|
| 2023 |
Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius F, Gordon M, Yang W, Coventry B, Hicks DR, ... ... Baker D, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Biorxiv : the Preprint Server For Biology. PMID 36993355 DOI: 10.1101/2023.03.14.532666 |
0.378 |
|
| 2023 |
Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, ... Baker D, et al. De novo design of small beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America. 120: e2207974120. PMID 36897987 DOI: 10.1073/pnas.2207974120 |
0.644 |
|
| 2023 |
Wang JYJ, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, ... ... Baker D, et al. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proceedings of the National Academy of Sciences of the United States of America. 120: e2214556120. PMID 36888664 DOI: 10.1073/pnas.2214556120 |
0.686 |
|
| 2023 |
Yeh AH, Norn C, Kipnis Y, Tischer D, Pellock SJ, Evans D, Ma P, Lee GR, Zhang JZ, Anishchenko I, Coventry B, Cao L, Dauparas J, Halabiya S, DeWitt M, ... ... Baker D, et al. De novo design of luciferases using deep learning. Nature. 614: 774-780. PMID 36813896 DOI: 10.1038/s41586-023-05696-3 |
0.817 |
|
| 2023 |
Nieweglowska ES, Brilot AF, Méndez-Moran M, Kokontis C, Baek M, Li J, Cheng Y, Baker D, Bondy-Denomy J, Agard DA. The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Nature Communications. 14: 927. PMID 36807264 DOI: 10.1038/s41467-023-36526-9 |
0.465 |
|
| 2023 |
Gerben SR, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. Design of Diverse Asymmetric Pockets in Homo-oligomeric Proteins. Biochemistry. 62: 358-368. PMID 36627259 DOI: 10.1021/acs.biochem.2c00497 |
0.431 |
|
| 2023 |
Lin D, Li X, Moult E, Park P, Tang B, Shen H, Grimm JB, Falco N, Jia BZ, Baker D, Lavis LD, Cohen AE. Time-tagged ticker tapes for intracellular recordings. Nature Biotechnology. PMID 36593408 DOI: 10.1038/s41587-022-01524-7 |
0.363 |
|
| 2022 |
Bermeo S, Favor A, Chang YT, Norris A, Boyken SE, Hsia Y, Haddox HK, Xu C, Brunette TJ, Wysocki VH, Bhabha G, Ekiert DC, Baker D. De novo design of obligate ABC-type heterotrimeric proteins. Nature Structural & Molecular Biology. 29: 1266-1276. PMID 36522429 DOI: 10.1038/s41594-022-00879-4 |
0.65 |
|
| 2022 |
Linsky TW, Noble K, Tobin AR, Crow R, Carter L, Urbauer JL, Baker D, Strauch EM. Sampling of structure and sequence space of small protein folds. Nature Communications. 13: 7151. PMID 36418330 DOI: 10.1038/s41467-022-34937-8 |
0.79 |
|
| 2022 |
Said MY, Kang CS, Wang S, Sheffler W, Salveson PJ, Bera AK, Kang A, Nguyen H, Ballard R, Li X, Bai H, Stewart L, Levine P, Baker D. Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks. Chemistry of Materials : a Publication of the American Chemical Society. 34: 9736-9744. PMID 36397834 DOI: 10.1021/acs.chemmater.2c02597 |
0.781 |
|
| 2022 |
Linder J, La Fleur A, Chen Z, Ljubeti A, Baker D, Kannan S, Seelig G. Interpreting Neural Networks for Biological Sequences by Learning Stochastic Masks. Nature Machine Intelligence. 4: 41-54. PMID 35966405 DOI: 10.1038/s42256-021-00428-6 |
0.678 |
|
| 2022 |
Wang J, Lisanza S, Juergens D, Tischer D, Watson JL, Castro KM, Ragotte R, Saragovi A, Milles LF, Baek M, Anishchenko I, Yang W, Hicks DR, Expòsit M, Schlichthaerle T, ... ... Baker D, et al. Scaffolding protein functional sites using deep learning. Science (New York, N.Y.). 377: 387-394. PMID 35862514 DOI: 10.1126/science.abn2100 |
0.679 |
|
| 2022 |
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, ... ... Baker D, et al. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. PMID 35667008 DOI: 10.1021/acs.jctc.2c00500 |
0.787 |
|
| 2022 |
Zhang JZ, Yeh HW, Walls AC, Wicky BIM, Sprouse KR, VanBlargan LA, Treger R, Quijano-Rubio A, Pham MN, Kraft JC, Haydon IC, Yang W, DeWitt M, Bowen JE, Chow CM, ... ... Baker D, et al. Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Nature Biotechnology. PMID 35484405 DOI: 10.1038/s41587-022-01280-8 |
0.742 |
|
| 2022 |
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, ... ... Baker D, et al. Multivalent designed proteins neutralize SARS-CoV-2 variants of concern and confer protection against infection in mice. Science Translational Medicine. eabn1252. PMID 35412328 DOI: 10.1126/scitranslmed.abn1252 |
0.773 |
|
| 2022 |
Cao L, Coventry B, Goreshnik I, Huang B, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, ... ... Baker D, et al. Design of protein binding proteins from target structure alone. Nature. PMID 35332283 DOI: 10.1038/s41586-022-04654-9 |
0.79 |
|
| 2022 |
Levine PM, Craven TW, Li X, Balana AT, Bird GH, Godes M, Salveson PJ, Erickson PW, Lamb M, Ahlrichs M, Murphy M, Ogohara C, Said MY, Walensky LD, Pratt MR, ... Baker D, et al. Generation of Potent and Stable GLP-1 Analogues Via "Serine Ligation". Acs Chemical Biology. PMID 35319882 DOI: 10.1021/acschembio.2c00075 |
0.747 |
|
| 2022 |
Singer JM, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku TM, Ford A, Ho E, ... ... Baker D, et al. Large-scale design and refinement of stable proteins using sequence-only models. Plos One. 17: e0265020. PMID 35286324 DOI: 10.1371/journal.pone.0265020 |
0.818 |
|
| 2022 |
Bhattacharya N, Thomas N, Rao R, Dauparas J, Koo PK, Baker D, Song YS, Ovchinnikov S. Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27: 34-45. PMID 34890134 |
0.625 |
|
| 2021 |
Legler PM, Little SF, Senft J, Schokman R, Carra JH, Compton JR, Chabot D, Tobery S, Fetterer DP, Siegel JB, Baker D, Friedlander AM. Treatment of experimental anthrax with pegylated circularly permuted capsule depolymerase. Science Translational Medicine. 13: eabh1682. PMID 34878819 DOI: 10.1126/scitranslmed.abh1682 |
0.463 |
|
| 2021 |
Anishchenko I, Pellock SJ, Chidyausiku TM, Ramelot TA, Ovchinnikov S, Hao J, Bafna K, Norn C, Kang A, Bera AK, DiMaio F, Carter L, Chow CM, Montelione GT, Baker D. De novo protein design by deep network hallucination. Nature. PMID 34853475 DOI: 10.1038/s41586-021-04184-w |
0.646 |
|
| 2021 |
Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Baker D, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7 |
0.786 |
|
| 2021 |
Humphreys IR, Pei J, Baek M, Krishnakumar A, Anishchenko I, Ovchinnikov S, Zhang J, Ness TJ, Banjade S, Bagde SR, Stancheva VG, Li XH, Liu K, Zheng Z, Barrero DJ, ... ... Baker D, et al. Computed structures of core eukaryotic protein complexes. Science (New York, N.Y.). eabm4805. PMID 34762488 DOI: 10.1126/science.abm4805 |
0.666 |
|
| 2021 |
Zhao YT, Fallas JA, Saini S, Ueda G, Somasundaram L, Zhou Z, Xavier Raj I, Xu C, Carter L, Wrenn S, Mathieu J, Sellers DL, Baker D, Ruohola-Baker H. F-domain valency determines outcome of signaling through the angiopoietin pathway. Embo Reports. e53471. PMID 34698433 DOI: 10.15252/embr.202153471 |
0.527 |
|
| 2021 |
Guye KN, Shen H, Yaman MY, Liao GY, Baker D, Ginger DS. Importance of Substrate-Particle Repulsion for Protein-Templated Assembly of Metal Nanoparticles. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 34309385 DOI: 10.1021/acs.langmuir.1c01194 |
0.343 |
|
| 2021 |
Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, ... ... Baker D, et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.). PMID 34282049 DOI: 10.1126/science.abj8754 |
0.63 |
|
| 2021 |
Bryan CM, Rocklin GJ, Bick MJ, Ford A, Majri-Morrison S, Kroll AV, Miller CJ, Carter L, Goreshnik I, Kang A, DiMaio F, Tarbell KV, Baker D. Computational design of a synthetic PD-1 agonist. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34272285 DOI: 10.1073/pnas.2102164118 |
0.708 |
|
| 2021 |
Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, ... ... Baker D, et al. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. Biorxiv : the Preprint Server For Biology. PMID 34268509 DOI: 10.1101/2021.07.07.451375 |
0.764 |
|
| 2021 |
Zhang JZ, Yeh HW, Walls AC, Wicky BIM, Sprouse K, VanBlargan LA, Treger R, Quijano-Rubio A, Pham MN, Kraft JC, Haydon IC, Yang W, DeWitt M, Chow C, Carter L, ... ... Baker D, et al. Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system. Biorxiv : the Preprint Server For Biology. PMID 34189528 DOI: 10.1101/2021.06.22.449355 |
0.739 |
|
| 2021 |
Koga N, Koga R, Liu G, Castellanos J, Montelione GT, Baker D. Role of backbone strain in de novo design of complex α/β protein structures. Nature Communications. 12: 3921. PMID 34168113 DOI: 10.1038/s41467-021-24050-7 |
0.62 |
|
| 2021 |
Yaman MY, Guye KN, Ziatdinov M, Shen H, Baker D, Kalinin SV, Ginger DS. Alignment of Au nanorods along designed protein nanofibers studied with automated image analysis. Soft Matter. PMID 34128040 DOI: 10.1039/d1sm00645b |
0.41 |
|
| 2021 |
Hosseinzadeh P, Watson PR, Craven TW, Li X, Rettie S, Pardo-Avila F, Bera AK, Mulligan VK, Lu P, Ford AS, Weitzner BD, Stewart LJ, Moyer AP, Di Piazza M, Whalen JG, ... ... Baker D, et al. Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nature Communications. 12: 3384. PMID 34099674 DOI: 10.1038/s41467-021-23609-8 |
0.809 |
|
| 2021 |
Hsia Y, Mout R, Sheffler W, Edman NI, Vulovic I, Park YJ, Redler RL, Bick MJ, Bera AK, Courbet A, Kang A, Brunette TJ, Nattermann U, Tsai E, Saleem A, ... ... Baker D, et al. Design of multi-scale protein complexes by hierarchical building block fusion. Nature Communications. 12: 2294. PMID 33863889 DOI: 10.1038/s41467-021-22276-z |
0.717 |
|
| 2021 |
Divine R, Dang HV, Ueda G, Fallas JA, Vulovic I, Sheffler W, Saini S, Zhao YT, Raj IX, Morawski PA, Jennewein MF, Homad LJ, Wan YH, Tooley MR, Seeger F, ... ... Baker D, et al. Designed proteins assemble antibodies into modular nanocages. Science (New York, N.Y.). 372. PMID 33795432 DOI: 10.1126/science.abd9994 |
0.669 |
|
| 2021 |
Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, ... ... Baker D, et al. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723038 DOI: 10.1073/pnas.2012800118 |
0.758 |
|
| 2021 |
Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, Baker D, Ovchinnikov S. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33712545 DOI: 10.1073/pnas.2017228118 |
0.762 |
|
| 2021 |
Ben-Sasson AJ, Watson JL, Sheffler W, Johnson MC, Bittleston A, Somasundaram L, Decarreau J, Jiao F, Chen J, Mela I, Drabek AA, Jarrett SM, Blacklow SC, Kaminski CF, Hura GL, ... ... Baker D, et al. Author Correction: Design of biologically active binary protein 2D materials. Nature. PMID 33654323 DOI: 10.1038/s41586-021-03331-7 |
0.771 |
|
| 2021 |
Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. De novo design of modular and tunable protein biosensors. Nature. PMID 33503651 DOI: 10.1038/s41586-021-03258-z |
0.773 |
|
| 2021 |
Ben-Sasson AJ, Watson JL, Sheffler W, Johnson MC, Bittleston A, Somasundaram L, Decarreau J, Jiao F, Chen J, Mela I, Drabek AA, Jarrett SM, Blacklow SC, Kaminski CF, Hura GL, ... ... Baker D, et al. Design of biologically active binary protein 2D materials. Nature. PMID 33408408 DOI: 10.1038/s41586-020-03120-8 |
0.787 |
|
| 2020 |
Zhao YT, Fallas JA, Saini S, Ueda G, Somasundaram L, Zhou Z, Xavier I, Ehnes D, Xu C, Carter L, Wrenn S, Mathieu J, Sellers DL, Baker D, Ruohola-Baker H. F-domain valency determines outcome of signaling through the angiopoietin pathway. Biorxiv : the Preprint Server For Biology. PMID 33501432 DOI: 10.1101/2020.09.19.304188 |
0.538 |
|
| 2020 |
Divine R, Dang HV, Ueda G, Fallas JA, Vulovic I, Sheffler W, Saini S, Zhao YT, Raj IX, Morawski PA, Jennewein MF, Homad LJ, Wan YH, Tooley MR, Seeger F, ... ... Baker D, et al. Designed proteins assemble antibodies into modular nanocages. Biorxiv : the Preprint Server For Biology. PMID 33299994 DOI: 10.1101/2020.12.01.406611 |
0.666 |
|
| 2020 |
Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, Kuhlman B. Perturbing the energy landscape for improved packing during computational protein design. Proteins. PMID 33249652 DOI: 10.1002/prot.26030 |
0.612 |
|
| 2020 |
Caldwell SJ, Haydon IC, Piperidou N, Huang PS, Bick MJ, Sjöström HS, Hilvert D, Baker D, Zeymer C. Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Proceedings of the National Academy of Sciences of the United States of America. PMID 33203677 DOI: 10.1073/pnas.2008535117 |
0.807 |
|
| 2020 |
Mulligan VK, Kang CS, Sawaya MR, Rettie S, Li X, Antselovich I, Craven TW, Watkins AM, Labonte JW, DiMaio F, Yeates TO, Baker D. Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Science : a Publication of the Protein Society. PMID 33058266 DOI: 10.1002/pro.3974 |
0.719 |
|
| 2020 |
Wang LT, Pereira LS, Flores-Garcia Y, O'Connor J, Flynn BJ, Schön A, Hurlburt NK, Dillon M, Yang ASP, Fabra-García A, Idris AH, Mayer BT, Gerber MW, Gottardo R, Mason RD, ... ... Baker D, et al. A Potent Anti-Malarial Human Monoclonal Antibody Targets Circumsporozoite Protein Minor Repeats and Neutralizes Sporozoites in the Liver. Immunity. PMID 32946741 DOI: 10.1016/J.Immuni.2020.08.014 |
0.59 |
|
| 2020 |
Farrell DP, Anishchenko I, Shakeel S, Lauko A, Passmore LA, Baker D, DiMaio F. Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM. Iucrj. 7: 881-892. PMID 32939280 DOI: 10.1107/S2052252520009306 |
0.385 |
|
| 2020 |
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls AC, Park YJ, Strauch EM, Stewart L, Diamond MS, Veesler D, Baker D. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Science (New York, N.Y.). PMID 32907861 DOI: 10.1126/Science.Abd9909 |
0.773 |
|
| 2020 |
Xu C, Lu P, Gamal El-Din TM, Pei XY, Johnson MC, Uyeda A, Bick MJ, Xu Q, Jiang D, Bai H, Reggiano G, Hsia Y, Brunette TJ, Dou J, Ma D, ... Baker D, et al. Computational design of transmembrane pores. Nature. PMID 32848250 DOI: 10.1038/S41586-020-2646-5 |
0.806 |
|
| 2020 |
Basanta B, Bick MJ, Bera AK, Norn C, Chow CM, Carter LP, Goreshnik I, Dimaio F, Baker D. An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 32839327 DOI: 10.1073/Pnas.2005412117 |
0.451 |
|
| 2020 |
Lajoie MJ, Boyken SE, Salter AI, Bruffey J, Rajan A, Langan RA, Olshefsky A, Muhunthan V, Bick MJ, Gewe M, Quijano-Rubio A, Johnson J, Lenz G, Nguyen A, Pun S, ... ... Baker D, et al. Designed protein logic to target cells with precise combinations of surface antigens. Science (New York, N.Y.). PMID 32820060 DOI: 10.1126/Science.Aba6527 |
0.316 |
|
| 2020 |
Cao L, Goreshnik I, Coventry B, Case JB, Miller L, Kozodoy L, Chen RE, Carter L, Walls L, Park YJ, Stewart L, Diamond M, Veesler D, Baker D. De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Biorxiv : the Preprint Server For Biology. PMID 32793905 DOI: 10.1101/2020.08.03.234914 |
0.309 |
|
| 2020 |
Ueda G, Antanasijevic A, Fallas JA, Sheffler W, Copps J, Ellis D, Hutchinson GB, Moyer A, Yasmeen A, Tsybovsky Y, Park YJ, Bick MJ, Sankaran B, Gillespie RA, Brouwer PJ, ... ... Baker D, et al. Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens. Elife. 9. PMID 32748788 DOI: 10.7554/Elife.57659 |
0.694 |
|
| 2020 |
Quijano-Rubio A, Yeh HW, Park J, Lee H, Langan RA, Boyken SE, Lajoie MJ, Cao L, Chow CM, Miranda MC, Wi J, Hong HJ, Stewart L, Oh BH, Baker D. design of modular and tunable allosteric biosensors. Biorxiv : the Preprint Server For Biology. PMID 32743576 DOI: 10.1101/2020.07.18.206946 |
0.782 |
|
| 2020 |
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2 |
0.756 |
|
| 2020 |
Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, ... ... Baker D, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507 |
0.778 |
|
| 2020 |
Brunette TJ, Bick MJ, Hansen JM, Chow CM, Kollman JM, Baker D. Modular repeat protein sculpting using rigid helical junctions. Proceedings of the National Academy of Sciences of the United States of America. PMID 32245816 DOI: 10.1073/Pnas.1908768117 |
0.705 |
|
| 2020 |
Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, ... ... Baker D, et al. De novo design of protein logic gates. Science (New York, N.Y.). 368: 78-84. PMID 32241946 DOI: 10.1126/Science.Aay2790 |
0.728 |
|
| 2020 |
Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proceedings of the National Academy of Sciences of the United States of America. PMID 32188784 DOI: 10.1073/Pnas.1914808117 |
0.826 |
|
| 2020 |
VanAernum ZL, Busch F, Jones BJ, Jia M, Chen Z, Boyken SE, Sahasrabuddhe A, Baker D, Wysocki VH. Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry. Nature Protocols. PMID 32005983 DOI: 10.1038/S41596-019-0281-0 |
0.711 |
|
| 2020 |
Hellner B, Alamdari S, Pyles H, Zhang S, Prakash A, Sprenger KG, De Yoreo JJ, Baker D, Pfaendtner J, Baneyx F. Sequence-structure-binding relationships reveal adhesion behavior of the Car9 solid-binding peptide: an integrated experimental and simulation study. Journal of the American Chemical Society. PMID 31934768 DOI: 10.1021/Jacs.9B11617 |
0.343 |
|
| 2020 |
Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Improved protein structure prediction using predicted interresidue orientations. Proceedings of the National Academy of Sciences of the United States of America. PMID 31896580 DOI: 10.1073/Pnas.1914677117 |
0.695 |
|
| 2020 |
Ueda G, Antanasijevic A, Fallas JA, Sheffler W, Copps J, Ellis D, Hutchinson GB, Moyer A, Yasmeen A, Tsybovsky Y, Park Y, Bick MJ, Sankaran B, Gillespie RA, Brouwer PJ, ... ... Baker D, et al. Author response: Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens Elife. DOI: 10.7554/Elife.57659.Sa2 |
0.693 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009 |
0.744 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008 |
0.762 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007 |
0.745 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005 |
0.734 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004 |
0.742 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003 |
0.759 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002 |
0.751 |
|
| 2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... Baker D, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001 |
0.737 |
|
| 2020 |
Marx SK, Vorobieva A, Chow C, Craig JM, Kim HC, Abell SJ, Huang J, Gerben S, Baker D, Gundlach JH. de novo Design of Ion Conducting Transmembrane Protein Nanopores Biophysical Journal. 118: 483a-484a. DOI: 10.1016/J.Bpj.2019.11.2678 |
0.306 |
|
| 2019 |
Dou J, Goreshnik I, Bryan C, Baker D, Strauch EM. Parallelized identification of on- and off-target protein interactions. Molecular Systems Design & Engineering. 5: 349-357. PMID 35265342 DOI: 10.1039/c9me00118b |
0.772 |
|
| 2019 |
Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D. De novo design of a homo-trimeric amantadine-binding protein. Elife. 8. PMID 31854299 DOI: 10.7554/Elife.47839 |
0.818 |
|
| 2019 |
Cannon KA, Park RU, Boyken SE, Nattermann U, Yi S, Baker D, King NP, Yeates TO. Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineeringfig. Protein Science : a Publication of the Protein Society. PMID 31840320 DOI: 10.1002/Pro.3802 |
0.437 |
|
| 2019 |
Khatib F, Desfosses A, Koepnick B, Flatten J, Popović Z, Baker D, Cooper S, Gutsche I, Horowitz S. Building de novo cryo-electron microscopy structures collaboratively with citizen scientists. Plos Biology. 17: e3000472. PMID 31714936 DOI: 10.1371/Journal.Pbio.3000472 |
0.691 |
|
| 2019 |
Weitzner BD, Kipnis Y, Daniel AG, Hilvert D, Baker D. A computational method for design of connected catalytic networks in proteins. Protein Science : a Publication of the Protein Society. PMID 31642127 DOI: 10.1002/Pro.3757 |
0.758 |
|
| 2019 |
Brouwer PJM, Antanasijevic A, Berndsen Z, Yasmeen A, Fiala B, Bijl TPL, Bontjer I, Bale JB, Sheffler W, Allen JD, Schorcht A, Burger JA, Camacho M, Ellis D, Cottrell CA, ... ... Baker D, et al. Enhancing and shaping the immunogenicity of native-like HIV-1 envelope trimers with a two-component protein nanoparticle. Nature Communications. 10: 4272. PMID 31537780 DOI: 10.1038/S41467-019-12080-1 |
0.669 |
|
| 2019 |
Foight GW, Wang Z, Wei CT, Jr Greisen P, Warner KM, Cunningham-Bryant D, Park K, Brunette TJ, Sheffler W, Baker D, Maly DJ. Multi-input chemical control of protein dimerization for programming graded cellular responses. Nature Biotechnology. PMID 31501561 DOI: 10.1038/S41587-019-0242-8 |
0.698 |
|
| 2019 |
Porter KA, Padhorny D, Desta I, Ignatov M, Beglov D, Kotelnikov S, Sun Z, Alekseenko A, Anishchenko I, Cong Q, Ovchinnikov S, Baker D, Vajda S, Kozakov D. Template-Based Modeling by ClusPro in CASP13 and the Potential for Using Co-evolutionary Information in Docking. Proteins. PMID 31444975 DOI: 10.1002/Prot.25808 |
0.633 |
|
| 2019 |
Pecora de Barros E, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 31442033 DOI: 10.1021/Acs.Jctc.9B00483 |
0.406 |
|
| 2019 |
Langan RA, Boyken SE, Ng AH, Samson JA, Dods G, Westbrook AM, Nguyen TH, Lajoie MJ, Chen Z, Berger S, Mulligan VK, Dueber JE, Novak WRP, El-Samad H, Baker D. De novo design of bioactive protein switches. Nature. PMID 31341284 DOI: 10.1038/S41586-019-1432-8 |
0.745 |
|
| 2019 |
Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H. Modular and tunable biological feedback control using a de novo protein switch. Nature. PMID 31341280 DOI: 10.1038/S41586-019-1425-7 |
0.344 |
|
| 2019 |
Park H, Lee GR, Kim DE, Anishchanka I, Cong Q, Baker D. High-accuracy refinement using Rosetta in CASP13. Proteins. PMID 31325340 DOI: 10.1002/Prot.25784 |
0.37 |
|
| 2019 |
Cong Q, Anishchenko I, Ovchinnikov S, Baker D. Protein interaction networks revealed by proteome coevolution. Science (New York, N.Y.). 365: 185-189. PMID 31296772 DOI: 10.1126/Science.Aaw6718 |
0.668 |
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| 2019 |
Pyles H, Zhang S, De Yoreo JJ, Baker D. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature. 571: 251-256. PMID 31292559 DOI: 10.1038/S41586-019-1361-6 |
0.436 |
|
| 2019 |
Wu Q, Peng Z, Anishchenko I, Cong Q, Baker D, Yang J. Protein contact prediction using metagenome sequence data and residual neural networks. Bioinformatics (Oxford, England). PMID 31173061 DOI: 10.1093/Bioinformatics/Btz477 |
0.347 |
|
| 2019 |
Koepnick B, Flatten J, Husain T, Ford A, Silva DA, Bick MJ, Bauer A, Liu G, Ishida Y, Boykov A, Estep RD, Kleinfelter S, Nørgård-Solano T, Wei L, Players F, ... Baker D, et al. De novo protein design by citizen scientists. Nature. PMID 31168091 DOI: 10.1038/S41586-019-1274-4 |
0.748 |
|
| 2019 |
Cao L, Yu B, Kong D, Cong Q, Yu T, Chen Z, Hu Z, Chang H, Zhong J, Baker D, He Y. Functional expression and characterization of the envelope glycoprotein E1E2 heterodimer of hepatitis C virus. Plos Pathogens. 15: e1007759. PMID 31116791 DOI: 10.1371/Journal.Ppat.1007759 |
0.662 |
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| 2019 |
Boyken SE, Benhaim MA, Busch F, Jia M, Bick MJ, Choi H, Klima JC, Chen Z, Walkey C, Mileant A, Sahasrabuddhe A, Wei KY, Hodge EA, Byron S, Quijano-Rubio A, ... Baker D, et al. De novo design of tunable, pH-driven conformational changes. Science (New York, N.Y.). 364: 658-664. PMID 31097662 DOI: 10.1126/Science.Aav7897 |
0.718 |
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| 2019 |
Bulutoglu B, Macazo FC, Bale J, King N, Baker D, Minteer SD, Banta S. Multimerization of an Alcohol Dehydrogenase by Fusion to a Designed Self-Assembling Protein Results in Enhanced Bioelectrocatalytic Operational Stability. Acs Applied Materials & Interfaces. PMID 31066271 DOI: 10.1021/Acsami.9B04256 |
0.366 |
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| 2019 |
Chen Z, Johnson MC, Chen J, Bick MJ, Boyken SE, Lin B, De Yoreo JJ, Kollman JM, Baker D, DiMaio F. Self-assembling 2D arrays with de novo protein building blocks. Journal of the American Chemical Society. PMID 31050411 DOI: 10.1021/Jacs.9B01978 |
0.789 |
|
| 2019 |
Basak S, Nobrega RP, Tavella D, Deveau LM, Koga N, Tatsumi-Koga R, Baker D, Massi F, Matthews CR. Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein. Proceedings of the National Academy of Sciences of the United States of America. PMID 30877249 DOI: 10.1073/Pnas.1818744116 |
0.383 |
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| 2019 |
Marcandalli J, Fiala B, Ols S, Perotti M, de van der Schueren W, Snijder J, Hodge E, Benhaim M, Ravichandran R, Carter L, Sheffler W, Brunner L, Lawrenz M, Dubois P, Lanzavecchia A, ... ... Baker D, et al. Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus. Cell. 176: 1420-1431.e17. PMID 30849373 DOI: 10.1016/J.Cell.2019.01.046 |
0.68 |
|
| 2019 |
Baker DA. What has de novo protein design taught us about protein folding and biophysics? Protein Science : a Publication of the Protein Society. PMID 30746840 DOI: 10.1002/Pro.3588 |
0.439 |
|
| 2019 |
Anderson CE, Buser JR, Fleming AM, Strauch EM, Ladd PD, Englund J, Baker D, Yager P. An integrated device for the rapid and sensitive detection of the influenza hemagglutinin. Lab On a Chip. PMID 30724293 DOI: 10.1039/C8Lc00691A |
0.725 |
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| 2019 |
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, ... ... Baker D, et al. De novo design of potent and selective mimics of IL-2 and IL-15. Nature. 565: 186-191. PMID 30626941 DOI: 10.2210/Pdb6Dg5/Pdb |
0.777 |
|
| 2019 |
Chen Z, Boyken SE, Jia M, Busch F, Flores-Solis D, Bick MJ, Lu P, VanAernum ZL, Sahasrabuddhe A, Langan RA, Bermeo S, Brunette TJ, Mulligan VK, Carter LP, DiMaio F, ... ... Baker D, et al. Programmable design of orthogonal protein heterodimers. Nature. 565: 106-111. PMID 30568301 DOI: 10.1038/s41586-018-0802-y |
0.809 |
|
| 2019 |
Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D. Author response: De novo design of a homo-trimeric amantadine-binding protein Elife. DOI: 10.7554/Elife.47839.Sa2 |
0.796 |
|
| 2019 |
Baker D. Computationally designed protein activation National Science Review. 6: 609-610. DOI: 10.1093/Nsr/Nwz063 |
0.36 |
|
| 2018 |
Day AL, Greisen P, Doyle L, Schena A, Stella N, Johnsson K, Baker D, Stoddard B. Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold. Protein Engineering, Design & Selection : Peds. PMID 30566669 DOI: 10.1093/Protein/Gzy031 |
0.392 |
|
| 2018 |
Romero Romero ML, Yang F, Lin YR, Toth-Petroczy A, Berezovsky IN, Goncearenco A, Yang W, Wellner A, Kumar-Deshmukh F, Sharon M, Baker D, Varani G, Tawfik DS. Simple yet functional phosphate-loop proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 30504143 DOI: 10.1073/Pnas.1812400115 |
0.362 |
|
| 2018 |
Shen H, Fallas JA, Lynch E, Sheffler W, Parry B, Jannetty N, Decarreau J, Wagenbach M, Vicente JJ, Chen J, Wang L, Dowling Q, Oberdorfer G, Stewart L, Wordeman L, ... Baker D, et al. De novo design of self-assembling helical protein filaments. Science (New York, N.Y.). 362: 705-709. PMID 30409885 DOI: 10.2210/Pdb6E9R/Pdb |
0.822 |
|
| 2018 |
Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivón LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D. De novo design of a non-local β-sheet protein with high stability and accuracy. Nature Structural & Molecular Biology. PMID 30374087 DOI: 10.1038/s41594-018-0141-6 |
0.791 |
|
| 2018 |
Maguire JB, Boyken SE, Baker D, Kuhlman B. Correction to Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design. Journal of Chemical Theory and Computation. PMID 30221938 DOI: 10.1021/Acs.Jctc.8B00883 |
0.564 |
|
| 2018 |
Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, ... Baker D, et al. De novo design of a fluorescence-activating β-barrel. Nature. PMID 30209393 DOI: 10.1038/S41586-018-0509-0 |
0.81 |
|
| 2018 |
Buchko GW, Pulavarti SVSRK, Ovchinnikov V, Shaw EA, Rettie SA, Myler PJ, Karplus M, Szyperski T, Baker D, Bahl CD. Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide-rich de novo designed peptides. Protein Science : a Publication of the Protein Society. PMID 30152054 DOI: 10.1002/Pro.3453 |
0.711 |
|
| 2018 |
Lau YK, Baytshtok V, Howard TA, Fiala BM, Morgan JM, Carter LP, Baker D, Lima CD, Bahl CD. Discovery and engineering of enhanced SUMO protease enzymes. The Journal of Biological Chemistry. PMID 29976752 DOI: 10.1074/Jbc.Ra118.004146 |
0.734 |
|
| 2018 |
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Baker D, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8 |
0.809 |
|
| 2018 |
Geiger-Schuller K, Sforza K, Yuhas M, Parmeggiani F, Baker D, Barrick D. Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions. Proceedings of the National Academy of Sciences of the United States of America. PMID 29959204 DOI: 10.1073/Pnas.1800283115 |
0.436 |
|
| 2018 |
Maguire JB, Boyken SE, Baker D, Kuhlman B. Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design. Journal of Chemical Theory and Computation. PMID 29652499 DOI: 10.1021/Acs.Jctc.8B00033 |
0.589 |
|
| 2018 |
Crook ZR, Sevilla GP, Friend D, Brusniak MY, Bandaranayake AD, Clarke M, Gewe M, Mhyre AJ, Baker D, Strong RK, Bradley P, Olson JM. Publisher Correction: Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets. Nature Communications. 9: 1072. PMID 29523778 DOI: 10.1038/S41467-018-03350-5 |
0.512 |
|
| 2018 |
Sutherland MC, Jarodsky JM, Ovchinnikov S, Baker D, Kranz RG. Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis. Journal of Molecular Biology. PMID 29518410 DOI: 10.1016/J.Jmb.2018.01.022 |
0.634 |
|
| 2018 |
Park H, Ovchinnikov S, Kim DE, DiMaio F, Baker D. Protein homology model refinement by large-scale energy optimization. Proceedings of the National Academy of Sciences of the United States of America. PMID 29507254 DOI: 10.1073/Pnas.1719115115 |
0.651 |
|
| 2018 |
Lu P, Min D, DiMaio F, Wei KY, Vahey MD, Boyken SE, Chen Z, Fallas JA, Ueda G, Sheffler W, Mulligan VK, Xu W, Bowie JU, Baker D. Accurate computational design of multipass transmembrane proteins. Science (New York, N.Y.). 359: 1042-1046. PMID 29496880 DOI: 10.1126/Science.Aaq1739 |
0.808 |
|
| 2018 |
Silva DA, Stewart L, Lam KH, Jin R, Baker D. Structures and disulfide cross-linking of de novo designed therapeutic mini-proteins. The Febs Journal. PMID 29389072 DOI: 10.1111/Febs.14394 |
0.463 |
|
| 2018 |
Sahasrabuddhe A, Hsia Y, Busch F, Sheffler W, King NP, Baker D, Wysocki VH. Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS. Proceedings of the National Academy of Sciences of the United States of America. PMID 29351988 DOI: 10.1073/Pnas.1713646115 |
0.743 |
|
| 2018 |
Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivón LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D. De novo design of a non-local beta-sheet protein with high stability and accuracy Nature Structural & Molecular Biology. 25: 1028-1034. DOI: 10.2210/Pdb6E5C/Pdb |
0.787 |
|
| 2018 |
Chen Z, Flores-Solis D, Sgourakis NG, Baker D. De Novo Design of a Protein Heterodimer with Specificity Mediated by Hydrogen Bond Networks Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb6Dmp/Pdb |
0.628 |
|
| 2018 |
Buchko G, Bahl C, Baker D. Chemical shifts for the de novo mini protein gHH_44 in the reduced state. Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr27420 |
0.701 |
|
| 2018 |
Pulavarti SVSRK, Shaw E, Bahl C, Garry B, Baker D, Szyperski T. Backbone 1H, 13C, and 15N Chemical Shift Assignments for gHEEE_02 in presence of 10 mM TCEP Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr27269 |
0.646 |
|
| 2017 |
Crook ZR, Sevilla GP, Friend D, Brusniak MY, Bandaranayake AD, Clarke M, Gewe M, Mhyre AJ, Baker D, Strong RK, Bradley P, Olson JM. Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets. Nature Communications. 8: 2244. PMID 29269835 DOI: 10.1038/S41467-017-02098-8 |
0.548 |
|
| 2017 |
Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D. Comprehensive computational design of ordered peptide macrocycles. Science (New York, N.Y.). 358: 1461-1466. PMID 29242347 DOI: 10.1126/Science.Aap7577 |
0.384 |
|
| 2017 |
Butterfield GL, Lajoie MJ, Gustafson HH, Sellers DL, Nattermann U, Ellis D, Bale JB, Ke S, Lenz GH, Yehdego A, Ravichandran R, Pun SH, King NP, Baker D. Evolution of a designed protein assembly encapsulating its own RNA genome. Nature. PMID 29236688 DOI: 10.1038/Nature25157 |
0.339 |
|
| 2017 |
McReynolds JR, Doncheck EM, Li Y, Vranjkovic O, Graf EN, Ogasawara D, Cravatt BF, Baker DA, Liu QS, Hillard CJ, Mantsch JR. Stress Promotes Drug Seeking Through Glucocorticoid-Dependent Endocannabinoid Mobilization in the Prelimbic Cortex. Biological Psychiatry. PMID 29100630 DOI: 10.1016/J.Biopsych.2017.09.024 |
0.305 |
|
| 2017 |
Younger D, Berger S, Baker D, Klavins E. High-throughput characterization of protein-protein interactions by reprogramming yeast mating. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087945 DOI: 10.1073/Pnas.1705867114 |
0.36 |
|
| 2017 |
Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 29069529 DOI: 10.1002/Cphc.201701147 |
0.34 |
|
| 2017 |
Dou J, Doyle L, Greisen PJ, Schena A, Park H, Johnsson K, Stoddard BL, Baker D. Sampling and Energy Evaluation Challenges in Ligand Binding Protein Design. Protein Science : a Publication of the Protein Society. PMID 28980354 DOI: 10.1002/Pro.3317 |
0.41 |
|
| 2017 |
Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva DA, Baker D, DeGrado WF. De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973862 DOI: 10.1073/Pnas.1710695114 |
0.466 |
|
| 2017 |
Chevalier A, Silva DA, Rocklin GJ, Hicks DR, Vergara R, Murapa P, Bernard SM, Zhang L, Lam KH, Yao G, Bahl CD, Miyashita SI, Goreshnik I, Fuller JT, Koday MT, ... Baker D, et al. Massively parallel de novo protein design for targeted therapeutics. Nature. PMID 28953867 DOI: 10.1038/Nature23912 |
0.818 |
|
| 2017 |
Ovchinnikov S, Park H, Kim D, DiMaio F, Baker D. Protein structure prediction using Rosetta in CASP12. Proteins. PMID 28940798 DOI: 10.1002/Prot.25390 |
0.675 |
|
| 2017 |
Bick MJ, Greisen PJ, Morey KJ, Antunes MS, La D, Sankaran B, Reymond L, Johnsson K, Medford JI, Baker D. Computational design of environmental sensors for the potent opioid fentanyl. Elife. 6. PMID 28925919 DOI: 10.7554/Elife.28909 |
0.376 |
|
| 2017 |
Park H, Kim D, Ovchinnikov S, Baker D, DiMaio F. Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins. PMID 28913931 DOI: 10.1002/Prot.25387 |
0.66 |
|
| 2017 |
Yeh CT, Brunette TJ, Baker D, McIntosh-Smith S, Parmeggiani F. Elfin: an algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. Journal of Structural Biology. PMID 28890160 DOI: 10.1016/J.Jsb.2017.09.001 |
0.455 |
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| 2017 |
Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, ... Baker D, et al. First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. Proceedings of the National Academy of Sciences of the United States of America. PMID 28864533 DOI: 10.1073/Pnas.1706907114 |
0.374 |
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| 2017 |
Lin YR, Koga N, Vorobiev SM, Baker D. Cyclic oligomer design with de novo αβ-proteins. Protein Science : a Publication of the Protein Society. PMID 28801928 DOI: 10.1002/Pro.3270 |
0.396 |
|
| 2017 |
Anishchenko I, Ovchinnikov S, Kamisetty H, Baker D. Origins of coevolution between residues distant in protein 3D structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28784799 DOI: 10.1073/Pnas.1702664114 |
0.674 |
|
| 2017 |
Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D. Global analysis of protein folding using massively parallel design, synthesis, and testing. Science (New York, N.Y.). 357: 168-175. PMID 28706065 DOI: 10.1126/Science.Aan0693 |
0.799 |
|
| 2017 |
Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature. PMID 28682307 DOI: 10.1038/Nature23314 |
0.618 |
|
| 2017 |
Strauch EM, Bernard SM, La D, Bohn AJ, Lee PS, Anderson CE, Nieusma T, Holstein CA, Garcia NK, Hooper KA, Ravichandran R, Nelson JW, Sheffler W, Bloom JD, Lee KK, ... Baker D, et al. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site. Nature Biotechnology. PMID 28604661 DOI: 10.1038/Nbt.3907 |
0.8 |
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| 2017 |
Simkovic F, Ovchinnikov S, Baker D, Rigden DJ. Applications of contact predictions to structural biology. Iucrj. 4: 291-300. PMID 28512576 DOI: 10.1107/S2052252517005115 |
0.662 |
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| 2017 |
Anderson CE, Holstein CA, Strauch EM, Bennett S, Chevalier A, Nelson JW, Fu E, Baker D, Yager P. A Rapid Diagnostic Assay for Intact Influenza Virus Using a High Affinity Hemagglutinin Binding Protein. Analytical Chemistry. PMID 28499086 DOI: 10.1021/Acs.Analchem.7B00769 |
0.789 |
|
| 2017 |
Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F, Cooper S. Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinformatics (Oxford, England). PMID 28481970 DOI: 10.1093/Bioinformatics/Btx283 |
0.801 |
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| 2017 |
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, ... Baker D, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125 |
0.801 |
|
| 2017 |
Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D. Computational design of self-assembling cyclic protein homo-oligomers. Nature Chemistry. 9: 353-360. PMID 28338692 DOI: 10.1038/nchem.2673 |
0.732 |
|
| 2017 |
Goldsmith M, Aggarwal N, Ashani Y, Jubran H, Greisen PJ, Ovchinnikov S, Leader H, Baker D, Sussman JL, Goldenzweig A, Fleishman SJ, Tawfik DS. Overcoming an optimization plateau in the directed evolution of highly efficient nerve agent bioscavengers. Protein Engineering, Design & Selection : Peds. 1-13. PMID 28159998 DOI: 10.1093/Protein/Gzx003 |
0.597 |
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| 2017 |
Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science (New York, N.Y.). 355: 294-298. PMID 28104891 DOI: 10.1126/Science.Aah4043 |
0.744 |
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| 2017 |
Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GV, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D, et al. Principles for designing proteins with cavities formed by curved β sheets. Science (New York, N.Y.). 355: 201-206. PMID 28082595 DOI: 10.1126/Science.Aah7389 |
0.379 |
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| 2017 |
Obexer R, Godina A, Garrabou X, Mittl PR, Baker D, Griffiths AD, Hilvert D. Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nature Chemistry. 9: 50-56. PMID 27995916 DOI: 10.1038/Nchem.2596 |
0.332 |
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| 2017 |
Shortridge MD, Hosseinzadeh P, Pardo-Avila F, Varani G, Baker D. Solution structure of de novo macrocycle design12_ss Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb6Be7/Pdb |
0.316 |
|
| 2017 |
Dang B, Wu H, Mulligan VK, Mravic M, Wu Y, Lemmin T, Ford A, Silva D, Baker D, DeGrado WF. De Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique Tertiary Structures Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb5V2G/Pdb |
0.314 |
|
| 2017 |
Lemak A, Rocklin GJ, Houliston S, Carter L, Chidyausiku TM, Baker D, Arrowsmith CH. Solution NMR structure of the de novo mini protein HEEH_rd4_0097 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb5Uyo/Pdb |
0.76 |
|
| 2017 |
Crook ZR, Bradley P, Sevilla G, Friend D, King C, Mhyre A, Strong R, Baker D, Olson JM. Abstract 5573: A high-affinity Optide (optimized peptide) inhibitor of the Hippo pathway’s YAP-TEAD interaction Cancer Research. 77: 5573-5573. DOI: 10.1158/1538-7445.Am2017-5573 |
0.561 |
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| 2017 |
Van Pattten WJ, Walder R, Adhikari A, Ravichandran R, Tinberg CE, Baker D, Perkins TT. A Computationally Designed Protein-Ligand Interaction is Mechanically Robust Biophysical Journal. 112: 455a. DOI: 10.1016/J.Bpj.2016.11.2440 |
0.355 |
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| 2017 |
Rocklin GJ, Chidyausiku T, Goreshnik I, Ford A, Houliston S, Arrowsmith C, Baker D. High-Throughput Protein Design Reveals Quantitative Protein Stability Requirements Biophysical Journal. 112: 194a. DOI: 10.1016/J.Bpj.2016.11.1076 |
0.797 |
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| 2017 |
Van Patten WJ, Walder R, Adhikari A, Okoniewski SR, Ravichandran R, Tinberg CE, Baker D, Perkins TT. Front Cover: Improved Free-Energy Landscape Quantification Illustrated with a Computationally Designed Protein-Ligand Interaction (ChemPhysChem 1/2018) Chemphyschem. 19: 1-1. DOI: 10.1002/Cphc.201701341 |
0.342 |
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| 2016 |
Mills JH, Sheffler W, Ener ME, Almhjell PJ, Oberdorfer G, Pereira JH, Parmeggiani F, Sankaran B, Zwart PH, Baker D. Computational design of a homotrimeric metalloprotein with a trisbipyridyl core. Proceedings of the National Academy of Sciences of the United States of America. PMID 27940918 DOI: 10.1073/Pnas.1600188113 |
0.811 |
|
| 2016 |
Rose JC, Huang PS, Camp ND, Ye J, Leidal AM, Goreshnik I, Trevillian BM, Dickinson MS, Cunningham-Bryant D, Debnath J, Baker D, Wolf-Yadlin A, Maly DJ. A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics. Nature Chemical Biology. PMID 27870838 DOI: 10.1038/Nchembio.2244 |
0.484 |
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| 2016 |
Berger S, Procko E, Margineantu D, Lee EF, Shen BW, Zelter A, Silva DA, Chawla K, Herold MJ, Garnier JM, Johnson R, MacCoss MJ, Lessene G, Davis TN, Stayton PS, ... ... Baker D, et al. Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife. 5. PMID 27805565 DOI: 10.7554/Elife.20352 |
0.381 |
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| 2016 |
Horowitz S, Koepnick B, Martin R, Tymieniecki A, Winburn AA, Cooper S, Flatten J, Rogawski DS, Koropatkin NM, Hailu TT, Jain N, Koldewey P, Ahlstrom LS, Chapman MR, Sikkema AP, ... ... Baker D, et al. Corrigendum: Determining crystal structures through crowdsourcing and coursework. Nature Communications. 7: 13392. PMID 27779204 DOI: 10.1038/Ncomms13392 |
0.65 |
|
| 2016 |
Park H, Bradley P, Greisen P, Liu Y, Mulligan VK, Kim DE, Baker D, DiMaio F. Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules. Journal of Chemical Theory and Computation. PMID 27766851 DOI: 10.1021/Acs.Jctc.6B00819 |
0.667 |
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| 2016 |
Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D. Corrigendum: Design of a hyperstable 60-subunit protein icosahedron. Nature. PMID 27760110 DOI: 10.1038/Nature20108 |
0.794 |
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| 2016 |
Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PR, Zerbe O, Baker D, Caflisch A, Plückthun A. Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. Journal of Molecular Biology. PMID 27664438 DOI: 10.1016/J.Jmb.2016.09.012 |
0.419 |
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| 2016 |
Horowitz S, Koepnick B, Martin R, Tymieniecki A, Winburn AA, Cooper S, Flatten J, Rogawski DS, Koropatkin NM, Hailu TT, Jain N, Koldewey P, Ahlstrom LS, Chapman MR, Sikkema AP, ... Baker D, et al. Determining crystal structures through crowdsourcing and coursework. Nature Communications. 7: 12549. PMID 27633552 DOI: 10.1038/Ncomms12549 |
0.698 |
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| 2016 |
Huang PS, Boyken SE, Baker D. The coming of age of de novo protein design. Nature. 537: 320-327. PMID 27629638 DOI: 10.1038/Nature19946 |
0.619 |
|
| 2016 |
Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen PJ, Rocklin GJ, Song Y, ... ... Baker D, et al. Accurate de novo design of hyperstable constrained peptides. Nature. PMID 27626386 DOI: 10.1038/Nature19791 |
0.795 |
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| 2016 |
Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D. Accurate design of megadalton-scale two-component icosahedral protein complexes. Science (New York, N.Y.). 353: 389-394. PMID 27463675 DOI: 10.1126/Science.Aaf8818 |
0.724 |
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| 2016 |
Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D. Design of a hyperstable 60-subunit protein icosahedron. Nature. PMID 27309817 DOI: 10.1038/Nature18010 |
0.817 |
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| 2016 |
Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. Corrigendum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nature Communications. 7: 11912. PMID 27271283 DOI: 10.1038/Ncomms11912 |
0.776 |
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| 2016 |
Rödström KE, Regenthal P, Bahl C, Ford A, Baker D, Lindkvist-Petersson K. Two common structural motifs for TCR recognition by staphylococcal enterotoxins. Scientific Reports. 6: 25796. PMID 27180909 DOI: 10.1038/Srep25796 |
0.691 |
|
| 2016 |
Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science (New York, N.Y.). 352: 680-7. PMID 27151862 DOI: 10.1126/Science.Aad8865 |
0.781 |
|
| 2016 |
Garcia KE, Babanova S, Scheffler W, Hans M, Baker D, Atanassov P, Banta S. Designed protein aggregates entrapping carbon nanotubes for bioelectrochemical oxygen reduction. Biotechnology and Bioengineering. PMID 27093643 DOI: 10.1002/Bit.25996 |
0.365 |
|
| 2016 |
Basanta B, Chan KK, Barth P, King T, Hinshaw JR, Sosnick TR, Liu G, Everett J, Xiao R, Montelione GT, Baker D. Introduction of a polar core into the de novo designed protein Top7. Protein Science : a Publication of the Protein Society. PMID 26873166 DOI: 10.1002/Pro.2899 |
0.619 |
|
| 2016 |
Ovchinnikov S, Park H, Kim DE, Liu Y, Yu-Ruei Wang R, Baker D. Structure Prediction using sparse simulated NOE restraints with Rosetta in CASP11. Proteins. PMID 26857542 DOI: 10.1002/Prot.25006 |
0.699 |
|
| 2016 |
Koday MT, Nelson J, Chevalier A, Koday M, Kalinoski H, Stewart L, Carter L, Nieusma T, Lee PS, Ward AB, Wilson IA, Dagley A, Smee DF, Baker D, Fuller DH. A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response. Plos Pathogens. 12: e1005409. PMID 26845438 DOI: 10.1371/Journal.Ppat.1005409 |
0.614 |
|
| 2016 |
Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S. Engineering an allosteric transcription factor to respond to new ligands. Nature Methods. 13: 177-83. PMID 26689263 DOI: 10.1038/Nmeth.3696 |
0.664 |
|
| 2016 |
Szyperski T, Pulavarti S, Shaw E, Bahl C, Garry B, Baker D. Solution structure of the de novo mini protein gHEEE_02 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr30312 |
0.714 |
|
| 2016 |
Crook ZR, Bradley P, King C, Mhyre AJ, Baker D, Olson JM. Abstract 2971: Optides (optimized knottin peptides) computationally designed to target the oncogenic HIPPO pathway Cancer Research. 76: 2971-2971. DOI: 10.1158/1538-7445.Am2016-2971 |
0.568 |
|
| 2016 |
Fuller DH, Koday MT, Nelson J, Chevalier A, Koday M, Smee DF, Hartman AL, Reed DS, Cole KS, Baker D. Computationally engineered influenza antiviral affords broad prophylactic and therapeutic protection against influenza Journal of Virus Eradication. 2: 8. DOI: 10.1016/S2055-6640(20)31112-2 |
0.556 |
|
| 2015 |
Feng J, Jester BW, Tinberg CE, Mandell DJ, Antunes MS, Chari R, Morey KJ, Rios X, Medford JI, Church GM, Fields S, Baker D. A general strategy to construct small molecule biosensors in eukaryotes. Elife. 4. PMID 26714111 DOI: 10.7554/Elife.10606 |
0.698 |
|
| 2015 |
Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D. Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into rosetta. Proteins. PMID 26677056 DOI: 10.1002/Prot.24974 |
0.793 |
|
| 2015 |
Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P. Rational design of α-helical tandem repeat proteins with closed architectures. Nature. PMID 26675735 DOI: 10.1038/Nature16191 |
0.662 |
|
| 2015 |
Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. Exploring the repeat protein universe through computational protein design. Nature. PMID 26675729 DOI: 10.1038/Nature16162 |
0.638 |
|
| 2015 |
King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D. Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife. 4. PMID 26650357 DOI: 10.7554/Elife.11012 |
0.366 |
|
| 2015 |
Goldsmith M, Eckstein S, Ashani Y, Greisen P, Leader H, Sussman JL, Aggarwal N, Ovchinnikov S, Tawfik DS, Baker D, Thiermann H, Worek F. Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro. Archives of Toxicology. PMID 26612364 DOI: 10.1007/S00204-015-1626-2 |
0.597 |
|
| 2015 |
Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nature Communications. 6: 10005. PMID 26598135 DOI: 10.1038/Ncomms10005 |
0.781 |
|
| 2015 |
Huang PS, Feldmeier K, Parmeggiani F, Fernandez Velasco DA, Höcker B, Baker D. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chemical Biology. PMID 26595462 DOI: 10.1038/Nchembio.1966 |
0.617 |
|
| 2015 |
Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker D, Shendure J. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Research. PMID 26553805 DOI: 10.1093/Nar/Gkv1177 |
0.778 |
|
| 2015 |
Bednar D, Beerens K, Sebestova E, Bendl J, Khare S, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. Plos Computational Biology. 11: e1004556. PMID 26529612 DOI: 10.1371/Journal.Pcbi.1004556 |
0.591 |
|
| 2015 |
Holstein CA, Chevalier A, Bennett S, Anderson CE, Keniston K, Olsen C, Li B, Bales B, Moore DR, Fu E, Baker D, Yager P. Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers. Analytical and Bioanalytical Chemistry. PMID 26427504 DOI: 10.1007/S00216-015-9052-0 |
0.393 |
|
| 2015 |
Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. Journal of Chemical Information and Modeling. PMID 26419257 DOI: 10.1021/Acs.Jcim.5B00387 |
0.605 |
|
| 2015 |
Lin YR, Koga N, Tatsumi-Koga R, Liu G, Clouser AF, Montelione GT, Baker D. Control over overall shape and size in de novo designed proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 26396255 DOI: 10.1073/Pnas.1509508112 |
0.452 |
|
| 2015 |
Wolf C, Siegel JB, Tinberg C, Camarca A, Gianfrani C, Paski S, Guan R, Montelione GT, Baker D, Pultz IS. Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions. Journal of the American Chemical Society. PMID 26374198 DOI: 10.1021/Jacs.5B08325 |
0.559 |
|
| 2015 |
Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Large scale determination of previously unsolved protein structures using evolutionary information. Elife. 4. PMID 26335199 DOI: 10.7554/Elife.09248 |
0.684 |
|
| 2015 |
Heinisch T, Pellizzoni M, Dürrenberger M, Tinberg CE, Köhler V, Klehr J, Häussinger D, Baker D, Ward TR. Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design. Journal of the American Chemical Society. 137: 10414-9. PMID 26226626 DOI: 10.1021/Jacs.5B06622 |
0.39 |
|
| 2015 |
Park H, DiMaio F, Baker D. CASP11 refinement experiments with ROSETTA. Proteins. PMID 26205421 DOI: 10.1002/Prot.24862 |
0.392 |
|
| 2015 |
Bale JB, Park RU, Liu Y, Gonen S, Gonen T, Cascio D, King NP, Yeates TO, Baker D. Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression. Protein Science : a Publication of the Protein Society. PMID 26174163 DOI: 10.1002/Pro.2748 |
0.429 |
|
| 2015 |
Blok NB, Tan D, Wang RY, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T. Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proceedings of the National Academy of Sciences of the United States of America. PMID 26170309 DOI: 10.1073/Pnas.1500257112 |
0.605 |
|
| 2015 |
Poust S, Piety J, Bar-Even A, Baker D, Keasling J, Siegel J. Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction. Chembiochem : a European Journal of Chemical Biology. PMID 26109266 DOI: 10.1002/Cbic.201500228 |
0.58 |
|
| 2015 |
Gonen S, DiMaio F, Gonen T, Baker D. PROTEIN DESIGN. Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces. Science (New York, N.Y.). 348: 1365-8. PMID 26089516 DOI: 10.1126/Science.Aaa9897 |
0.415 |
|
| 2015 |
Matthaei JF, DiMaio F, Richards JJ, Pozzo LD, Baker D, Baneyx F. Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations. Nano Letters. PMID 25986921 DOI: 10.1021/Acs.Nanolett.5B01499 |
0.334 |
|
| 2015 |
Antala S, Ovchinnikov S, Kamisetty H, Baker D, Dempski RE. Computational modeling and functional studies provide a structural scaffold for the zinc transporter hZIP4. The Journal of Biological Chemistry. PMID 25971965 DOI: 10.1074/Jbc.M114.617613 |
0.668 |
|
| 2015 |
Park H, DiMaio F, Baker D. The origin of consistent protein structure refinement from structural averaging. Structure (London, England : 1993). 23: 1123-8. PMID 25960407 DOI: 10.1016/J.Str.2015.03.022 |
0.374 |
|
| 2015 |
O'Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. Journal of Chemical Theory and Computation. 11: 609-622. PMID 25866491 DOI: 10.1021/Ct500864R |
0.787 |
|
| 2015 |
Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB, Tran HM, Noor E, Gallaher JL, Bale J, Yoshikuni Y, Gelb MH, Keasling JD, ... ... Baker D, et al. Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences of the United States of America. 112: 3704-9. PMID 25775555 DOI: 10.1073/Pnas.1500545112 |
0.678 |
|
| 2015 |
Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H, Egelman EH, Basler M. Structure of the type VI secretion system contractile sheath. Cell. 160: 952-62. PMID 25723169 DOI: 10.1016/J.Cell.2015.01.037 |
0.611 |
|
| 2015 |
DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits TC, Cheng Y, Baker D. Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nature Methods. 12: 361-5. PMID 25707030 DOI: 10.1038/Nmeth.3286 |
0.76 |
|
| 2015 |
Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature Methods. 12: 335-8. PMID 25707029 DOI: 10.1038/Nmeth.3287 |
0.609 |
|
| 2015 |
Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW, Baker D, Stevens RC, Schultz PG. Transition states. Trapping a transition state in a computationally designed protein bottle. Science (New York, N.Y.). 347: 863-7. PMID 25700516 DOI: 10.1126/Science.Aaa2424 |
0.785 |
|
| 2015 |
Wijma HJ, Floor RJ, Bjelic S, Marrink SJ, Baker D, Janssen DB. Enantioselective enzymes by computational design and in silico screening. Angewandte Chemie (International Ed. in English). 54: 3726-30. PMID 25651000 DOI: 10.1002/Anie.201411415 |
0.34 |
|
| 2015 |
Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D, Conticello VP. Structural plasticity of helical nanotubes based on coiled-coil assemblies. Structure (London, England : 1993). 23: 280-9. PMID 25620001 DOI: 10.1016/J.Str.2014.12.008 |
0.76 |
|
| 2015 |
Morag O, Sgourakis NG, Baker D, Goldbourt A. The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope. Proceedings of the National Academy of Sciences of the United States of America. 112: 971-6. PMID 25587134 DOI: 10.1073/Pnas.1415393112 |
0.634 |
|
| 2015 |
Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Control of repeat-protein curvature by computational protein design. Nature Structural & Molecular Biology. 22: 167-74. PMID 25580576 DOI: 10.1038/Nsmb.2938 |
0.606 |
|
| 2015 |
Bergeron JR, Worrall LJ, De S, Sgourakis NG, Cheung AH, Lameignere E, Okon M, Wasney GA, Baker D, McIntosh LP, Strynadka NC. The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body. Structure (London, England : 1993). 23: 161-72. PMID 25533490 DOI: 10.1016/J.Str.2014.10.021 |
0.64 |
|
| 2015 |
Parmeggiani F, Huang PS, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J, Mao L, Janjua H, Montelione GT, Hunt J, Baker D. A general computational approach for repeat protein design. Journal of Molecular Biology. 427: 563-75. PMID 25451037 DOI: 10.1016/J.Jmb.2014.11.005 |
0.613 |
|
| 2015 |
Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins. 83: 309-17. PMID 25388768 DOI: 10.1002/Prot.24719 |
0.681 |
|
| 2015 |
Feng J, Jester BW, Tinberg CE, Mandell DJ, Antunes MS, Chari R, Morey KJ, Rios X, Medford JI, Church GM, Fields S, Baker D. Author response: A general strategy to construct small molecule biosensors in eukaryotes Elife. DOI: 10.7554/Elife.10606.018 |
0.666 |
|
| 2015 |
Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Author response: Large-scale determination of previously unsolved protein structures using evolutionary information Elife. DOI: 10.7554/Elife.09248.031 |
0.627 |
|
| 2015 |
Liu G, Lin Y, Koga N, Koga R, Xiao R, Janjua H, Pederson K, Acton TB, Kornhaber G, Everett JK, Baker D, Montelione GT. Solution NMR Structure of DE NOVO DESIGNED PROTEIN, Rossmann2x2 Fold, Northeast Structural Genomics Consortium (NESG) Target OR446 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2N3Z/Pdb |
0.354 |
|
| 2014 |
Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Research. 42: 13839-52. PMID 25389263 DOI: 10.1093/Nar/Gku1096 |
0.794 |
|
| 2014 |
Huang PS, Oberdorfer G, Xu C, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D. High thermodynamic stability of parametrically designed helical bundles. Science (New York, N.Y.). 346: 481-5. PMID 25342806 DOI: 10.1126/Science.1257481 |
0.742 |
|
| 2014 |
Liu DS, Nivón LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS, Ye AZ, Ellisman MH, Drennan CL, Baker D, Ting AY. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Proceedings of the National Academy of Sciences of the United States of America. 111: E4551-9. PMID 25313043 DOI: 10.1073/Pnas.1404736111 |
0.609 |
|
| 2014 |
Demers JP, Habenstein B, Loquet A, Kumar Vasa S, Giller K, Becker S, Baker D, Lange A, Sgourakis NG. High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy. Nature Communications. 5: 4976. PMID 25264107 DOI: 10.1038/Ncomms5976 |
0.659 |
|
| 2014 |
Liu Y, Zhang X, Tan YL, Bhabha G, Ekiert DC, Kipnis Y, Bjelic S, Baker D, Kelly JW. De novo-designed enzymes as small-molecule-regulated fluorescence imaging tags and fluorescent reporters. Journal of the American Chemical Society. 136: 13102-5. PMID 25209927 DOI: 10.1021/Ja5056356 |
0.311 |
|
| 2014 |
Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, Baker D, et al. A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell. 157: 1644-56. PMID 24949974 DOI: 10.1016/J.Cell.2014.04.034 |
0.544 |
|
| 2014 |
King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D. Accurate design of co-assembling multi-component protein nanomaterials. Nature. 510: 103-8. PMID 24870237 DOI: 10.1038/Nature13404 |
0.743 |
|
| 2014 |
Alushin GM, Lander GC, Kellogg EH, Zhang R, Baker D, Nogales E. High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell. 157: 1117-29. PMID 24855948 DOI: 10.1016/J.Cell.2014.03.053 |
0.734 |
|
| 2014 |
Chen KY, Sun J, Salvo JS, Baker D, Barth P. High-resolution modeling of transmembrane helical protein structures from distant homologues. Plos Computational Biology. 10: e1003636. PMID 24854015 DOI: 10.1371/Journal.Pcbi.1003636 |
0.662 |
|
| 2014 |
Preiswerk N, Beck T, Schulz JD, Milovník P, Mayer C, Siegel JB, Baker D, Hilvert D. Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Proceedings of the National Academy of Sciences of the United States of America. 111: 8013-8. PMID 24847076 DOI: 10.1073/Pnas.1401073111 |
0.626 |
|
| 2014 |
King C, Garza EN, Mazor R, Linehan JL, Pastan I, Pepper M, Baker D. Removing T-cell epitopes with computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 111: 8577-82. PMID 24843166 DOI: 10.1073/Pnas.1321126111 |
0.583 |
|
| 2014 |
Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Elife. 3: e02030. PMID 24842992 DOI: 10.7554/Elife.02030 |
0.676 |
|
| 2014 |
Mazor R, Eberle JA, Hu X, Vassall AN, Onda M, Beers R, Lee EC, Kreitman RJ, Lee B, Baker D, King C, Hassan R, Benhar I, Pastan I. Recombinant immunotoxin for cancer treatment with low immunogenicity by identification and silencing of human T-cell epitopes. Proceedings of the National Academy of Sciences of the United States of America. 111: 8571-6. PMID 24799704 DOI: 10.1073/Pnas.1405153111 |
0.513 |
|
| 2014 |
Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF, Baker D. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nature Chemical Biology. 10: 386-91. PMID 24705591 DOI: 10.1038/Nchembio.1498 |
0.739 |
|
| 2014 |
Wang Y, Khan IF, Boissel S, Jarjour J, Pangallo J, Thyme S, Baker D, Scharenberg AM, Rawlings DJ. Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. Nucleic Acids Research. 42: 6463-75. PMID 24682825 DOI: 10.1093/Nar/Gku224 |
0.786 |
|
| 2014 |
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, ... Baker D, et al. WeFold: a coopetition for protein structure prediction. Proteins. 82: 1850-68. PMID 24677212 DOI: 10.1002/Prot.24538 |
0.722 |
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| 2014 |
Baker D. Protein folding, structure prediction and design Biochemical Society Transactions. 42: 225-229. PMID 24646222 DOI: 10.1042/Bst20130055 |
0.412 |
|
| 2014 |
Liu Y, Tan YL, Zhang X, Bhabha G, Ekiert DC, Genereux JC, Cho Y, Kipnis Y, Bjelic S, Baker D, Kelly JW. Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts. Proceedings of the National Academy of Sciences of the United States of America. 111: 4449-54. PMID 24591605 DOI: 10.1073/Pnas.1323268111 |
0.391 |
|
| 2014 |
Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with rosetta Methods in Molecular Biology. 1123: 265-282. PMID 24510272 DOI: 10.1007/978-1-62703-968-0_17 |
0.76 |
|
| 2014 |
Wijma HJ, Floor RJ, Jekel PA, Baker D, Marrink SJ, Janssen DB. Computationally designed libraries for rapid enzyme stabilization Protein Engineering, Design and Selection. 27: 49-58. PMID 24402331 DOI: 10.1093/Protein/Gzt061 |
0.353 |
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| 2014 |
Mao B, Tejero R, Baker D, Montelione GT. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. Journal of the American Chemical Society. 136: 1893-906. PMID 24392845 DOI: 10.1021/Ja409845W |
0.344 |
|
| 2014 |
Strauch EM, Fleishman SJ, Baker D. Computational design of a pH-sensitive IgG binding protein. Proceedings of the National Academy of Sciences of the United States of America. 111: 675-80. PMID 24381156 DOI: 10.1073/Pnas.1313605111 |
0.77 |
|
| 2014 |
Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D, Scharenberg AM. MegaTALs: A rare-cleaving nuclease architecture for therapeutic genome engineering Nucleic Acids Research. 42: 2591-2601. PMID 24285304 DOI: 10.1093/Nar/Gkt1224 |
0.769 |
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| 2014 |
Thyme SB, Boissel SJ, Arshiya Quadri S, Nolan T, Baker DA, Park RU, Kusak L, Ashworth J, Baker D. Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Research. 42: 2564-76. PMID 24270794 DOI: 10.1093/Nar/Gkt1212 |
0.785 |
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| 2014 |
Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D. Relaxation of backbone bond geometry improves protein energy landscape modeling. Protein Science : a Publication of the Protein Society. 23: 47-55. PMID 24265211 DOI: 10.1002/Pro.2389 |
0.608 |
|
| 2014 |
Nivón LG, Bjelic S, King C, Baker D. Automating human intuition for protein design. Proteins. 82: 858-66. PMID 24265170 DOI: 10.1002/Prot.24463 |
0.6 |
|
| 2014 |
Bjelic S, Kipnis Y, Wang L, Pianowski Z, Vorobiev S, Su M, Seetharaman J, Xiao R, Kornhaber G, Hunt JF, Tong L, Hilvert D, Baker D. Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design. Journal of Molecular Biology. 426: 256-71. PMID 24161950 DOI: 10.1016/J.Jmb.2013.10.012 |
0.36 |
|
| 2014 |
Kim DE, Dimaio F, Yu-Ruei Wang R, Song Y, Baker D. One contact for every twelve residues allows robust and accurate topology-level protein structure modeling Proteins: Structure, Function and Bioinformatics. 82: 208-218. PMID 23900763 DOI: 10.1002/Prot.24374 |
0.592 |
|
| 2014 |
Ovchinnikov S, Kamisetty H, Baker D. Author response: Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information Elife. DOI: 10.7554/Elife.02030.014 |
0.625 |
|
| 2014 |
Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information Elife. 2014. DOI: 10.7554/eLife.02030 |
0.606 |
|
| 2014 |
Rossi P, Lange OF, Sgourakis NG, Song Y, Lee H, Aramini JM, Ertekin A, Xiao R, Acton TB, Baker D, Montelione GT. Solution NMR Structure of Maltose-binding protein from Escherichia coli, Northeast Structural Genomics Consortium (NESG) Target ER690 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Mv0/Pdb |
0.649 |
|
| 2014 |
Pulavarti SVSRK, Kipnis Y, Sukumaran D, Maglaqui M, Janjua H, Mao L, Xiao R, Kornhaber G, Baker D, Montelione GT, Szyperski T. Solution NMR Structure of De novo designed protein, Northeast Structural Genomics Consortium (NESG) Target OR459 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Mra/Pdb |
0.349 |
|
| 2014 |
Pulavarti SV, Nivon L, Maglaqui M, Janjua H, Mao L, Xiao R, Kornhaber G, Baker D, Montelione G, Szyperski T. Solution NMR Structure of De novo designed Protein, Northeast Structural Genomics Consortium (NESG) Target OR457 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr25061 |
0.796 |
|
| 2014 |
Terwilliger TC, DiMaio F, Read RJ, Baker D, Brunger AT, Adams PD, Afonine PV, Hung L. Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography Biophysical Journal. 106: 34a. DOI: 10.1016/J.Bpj.2013.11.263 |
0.389 |
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| 2014 |
Lai Y, King NP, Sheffler W, McNamara DE, Bale JB, Baker D, Yeates TO. Symmetry-Based Design and Structure of Self-Assembling Protein Cages and Nanomaterials Biophysical Journal. 106: 445a. DOI: 10.1016/J.Bpj.2013.11.2516 |
0.746 |
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| 2014 |
Kellogg EH, Alushin GM, Lander GC, Baker D, Nogales E. Studying the Structural Origins of Microtubule Dynamic Instability through Combining Computational Modeling and cryoEM Biophysical Journal. 106: 351a. DOI: 10.1016/J.Bpj.2013.11.1996 |
0.737 |
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| 2014 |
Obexer R, Studer S, Giger L, Pinkas DM, Grütter MG, Baker D, Hilvert D. Active site plasticity of a computationally designed retro-aldolase enzyme Chemcatchem. 6: 1043-1050. DOI: 10.1002/Cctc.201300933 |
0.367 |
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| 2013 |
Fang J, Mehlich A, Koga N, Huang J, Koga R, Gao X, Hu C, Jin C, Rief M, Kast J, Baker D, Li H. Forced protein unfolding leads to highly elastic and tough protein hydrogels. Nature Communications. 4: 2974. PMID 24352111 DOI: 10.1038/Ncomms3974 |
0.332 |
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| 2013 |
Wittenberg G, Sheffler W, Darchi D, Baker D, Noy D. Accelerated electron transport from photosystem I to redox partners by covalently linked ferredoxin. Physical Chemistry Chemical Physics : Pccp. 15: 19608-14. PMID 24129892 DOI: 10.1039/C3Cp53264J |
0.699 |
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| 2013 |
DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods. 10: 1102-4. PMID 24076763 DOI: 10.1107/S2053273314092171 |
0.311 |
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| 2013 |
Cherny I, Greisen P, Ashani Y, Khare SD, Oberdorfer G, Leader H, Baker D, Tawfik DS. Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries. Acs Chemical Biology. 8: 2394-403. PMID 24041203 DOI: 10.1021/Cb4004892 |
0.524 |
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| 2013 |
Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D. High-resolution comparative modeling with RosettaCM. Structure (London, England : 1993). 21: 1735-42. PMID 24035711 DOI: 10.1016/J.Str.2013.08.005 |
0.724 |
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| 2013 |
Cooper S, Khatib F, Baker D. Increasing public involvement in structural biology. Structure (London, England : 1993). 21: 1482-4. PMID 24010706 DOI: 10.1016/J.Str.2013.08.009 |
0.639 |
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| 2013 |
Kamisetty H, Ovchinnikov S, Baker D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era Proceedings of the National Academy of Sciences of the United States of America. 110: 15674-15679. PMID 24009338 DOI: 10.1073/Pnas.1314045110 |
0.671 |
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| 2013 |
Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 501: 212-6. PMID 24005320 DOI: 10.1038/Nature12443 |
0.747 |
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| 2013 |
Vernon R, Shen Y, Baker D, Lange OF. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker. Journal of Biomolecular Nmr. 57: 117-27. PMID 23975356 DOI: 10.1007/S10858-013-9772-4 |
0.547 |
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| 2013 |
Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. Journal of the American Chemical Society. 135: 13393-9. PMID 23924187 DOI: 10.1021/Ja403503M |
0.757 |
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| 2013 |
van der Schot G, Zhang Z, Vernon R, Shen Y, Vranken WF, Baker D, Bonvin AM, Lange OF. Improving 3D structure prediction from chemical shift data. Journal of Biomolecular Nmr. 57: 27-35. PMID 23912841 DOI: 10.1007/S10858-013-9762-6 |
0.607 |
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| 2013 |
Moal IH, Moretti R, Baker D, Fernández-Recio J. Scoring functions for protein-protein interactions. Current Opinion in Structural Biology. 23: 862-7. PMID 23871100 DOI: 10.1016/J.Sbi.2013.06.017 |
0.411 |
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| 2013 |
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... Baker D, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356 |
0.63 |
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| 2013 |
Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G, Hunt JF, Tong L, Montelione GT, Baker D. Computational design of a protein-based enzyme inhibitor. Journal of Molecular Biology. 425: 3563-75. PMID 23827138 DOI: 10.1016/J.Jmb.2013.06.035 |
0.417 |
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| 2013 |
Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, Hilvert D. Evolution of a designed retro-aldolase leads to complete active site remodeling Nature Chemical Biology. 9: 494-498. PMID 23748672 DOI: 10.1038/Nchembio.1276 |
0.363 |
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| 2013 |
Harger M, Zheng L, Moon A, Ager C, An JH, Choe C, Lai YL, Mo B, Zong D, Smith MD, Egbert RG, Mills JH, Baker D, Pultz IS, Siegel JB. Expanding the product profile of a microbial alkane biosynthetic pathway. Acs Synthetic Biology. 2: 59-62. PMID 23656326 DOI: 10.1021/Sb300061X |
0.718 |
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| 2013 |
Bergeron JR, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NC. A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. Plos Pathogens. 9: e1003307. PMID 23633951 DOI: 10.1371/Journal.Ppat.1003307 |
0.632 |
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| 2013 |
Pryce G, Cabranes A, Fernández-Ruiz J, Bisogno T, Di Marzo V, Long JZ, Cravatt BF, Giovannoni G, Baker D. Control of experimental spasticity by targeting the degradation of endocannabinoids using selective fatty acid amide hydrolase inhibitors. Multiple Sclerosis (Houndmills, Basingstoke, England). 19: 1896-904. PMID 23625705 DOI: 10.1177/1352458513485982 |
0.427 |
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| 2013 |
Geibel S, Procko E, Hultgren SJ, Baker D, Waksman G. Structural and energetic basis of folded-protein transport by the FimD usher. Nature. 496: 243-6. PMID 23579681 DOI: 10.1038/Nature12007 |
0.321 |
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| 2013 |
Nivón LG, Moretti R, Baker D. A Pareto-optimal refinement method for protein design scaffolds. Plos One. 8: e59004. PMID 23565140 DOI: 10.1371/Journal.Pone.0059004 |
0.815 |
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| 2013 |
Demers JP, Sgourakis NG, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A. The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles. Plos Pathogens. 9: e1003245. PMID 23555258 DOI: 10.1371/Journal.Ppat.1003245 |
0.651 |
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| 2013 |
Jardine J, Julien JP, Menis S, Ota T, Kalyuzhniy O, McGuire A, Sok D, Huang PS, MacPherson S, Jones M, Nieusma T, Mathison J, Baker D, Ward AB, Burton DR, et al. Rational HIV immunogen design to target specific germline B cell receptors. Science (New York, N.Y.). 340: 711-6. PMID 23539181 DOI: 10.1126/Science.1234150 |
0.492 |
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| 2013 |
Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angewandte Chemie (International Ed. in English). 52: 5700-25. PMID 23526810 DOI: 10.1002/Anie.201204077 |
0.519 |
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| 2013 |
Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics. 42: 265-87. PMID 23451892 DOI: 10.1146/Annurev-Biophys-083012-130253 |
0.547 |
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| 2013 |
Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, ... Baker D, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0 |
0.777 |
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| 2013 |
Whitehead TA, Baker D, Fleishman SJ. Computational design of novel protein binders and experimental affinity maturation. Methods in Enzymology. 523: 1-19. PMID 23422423 DOI: 10.1016/B978-0-12-394292-0.00001-1 |
0.377 |
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| 2013 |
Bjelic S, Nivón LG, Çelebi-Ölçüm N, Kiss G, Rosewall CF, Lovick HM, Ingalls EL, Gallaher JL, Seetharaman J, Lew S, Montelione GT, Hunt JF, Michael FE, Houk KN, Baker D. Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction. Acs Chemical Biology. 8: 749-57. PMID 23330600 DOI: 10.1021/Cb3006227 |
0.457 |
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| 2013 |
Kipnis Y, Baker D. Comparison of designed and randomly generated catalysts for simple chemical reactions. Protein Science : a Publication of the Protein Society. 21: 1388-95. PMID 22811380 DOI: 10.1002/Pro.2125 |
0.357 |
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| 2013 |
Liu G, Zanghellini AL, Chan K, Xiao R, Janjua H, Kogan S, Maglaqui M, Ciccosanti C, Acton TB, Kornhaber G, Everett JK, Baker D, Montelione GT. Solution NMR Structure of De novo designed Top7 Fold Protein Top7m13, Northeast Structural Genomics Consortium (NESG) Target OR33 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Mbl/Pdb |
0.354 |
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| 2013 |
Kosugi T, Koga N, Tatsumi-Koga R, Baker D. 1P089 Theoretical design of functionalized proteins with ideal scaffold(01F. Protein:Engineering,Poster) Seibutsu Butsuri. 53. DOI: 10.2142/Biophys.53.S120_5 |
0.318 |
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| 2013 |
Koga N, Koga(Tatsumi) R, Liu G, Xiao R, Montelione GT, Baker D. 1P088 Principles for designing ideal protein structures(01F. Protein:Engineering,Poster) Seibutsu Butsuri. 53: S120. DOI: 10.2142/Biophys.53.S120_4 |
0.377 |
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| 2013 |
Rossi P, Sgourakis N, Shi L, Liu G, Barbieri C, Lee H, Grant T, Luft J, Xiao R, Acton T, Montelione G, Snell E, Baker D, Lange O. Solution structure of the Aha1 dimer from Colwellia psychrerythraea Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr19235 |
0.6 |
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| 2013 |
Demers J, Sgourakis N, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A. 13C and 15N chemical shifts for Shigella Flexneri MxiH Type three secretion system needle subunit Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr18651 |
0.567 |
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| 2013 |
Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A. Remodeling a β-peptide bundle Chemical Science. 4: 319-324. DOI: 10.1039/C2Sc21117C |
0.505 |
|
| 2012 |
Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel JB. Computational design of an α-gliadin peptidase. Journal of the American Chemical Society. 134: 20513-20. PMID 23153249 DOI: 10.1021/Ja3094795 |
0.755 |
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| 2012 |
Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, Montelione GT, Baker D. Principles for designing ideal protein structures. Nature. 491: 222-7. PMID 23135467 DOI: 10.1038/Nature11600 |
0.421 |
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| 2012 |
Kellogg EH, Lange OF, Baker D. Evaluation and optimization of discrete state models of protein folding. The Journal of Physical Chemistry. B. 116: 11405-13. PMID 22958200 DOI: 10.1021/Jp3044303 |
0.699 |
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| 2012 |
Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJ, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, ... ... Baker D, et al. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Journal of the American Chemical Society. 134: 16197-206. PMID 22871159 DOI: 10.1021/Ja3037367 |
0.704 |
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| 2012 |
Tyka MD, Jung K, Baker D. Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. Journal of Computational Chemistry. 33: 2483-91. PMID 22847521 DOI: 10.1002/Jcc.23069 |
0.359 |
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| 2012 |
Alon A, Grossman I, Gat Y, Kodali VK, DiMaio F, Mehlman T, Haran G, Baker D, Thorpe C, Fass D. The dynamic disulphide relay of quiescin sulphydryl oxidase. Nature. 488: 414-8. PMID 22801504 DOI: 10.1038/Nature11267 |
0.369 |
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| 2012 |
Lange OF, Rossi P, Sgourakis NG, Song Y, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT, Baker D. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proceedings of the National Academy of Sciences of the United States of America. 109: 10873-8. PMID 22733734 DOI: 10.1073/Pnas.1203013109 |
0.732 |
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| 2012 |
Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Atomic model of the type III secretion system needle Nature. 486: 276-279. PMID 22699623 DOI: 10.1038/Nature11079 |
0.708 |
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| 2012 |
Khersonsky O, Kiss G, Röthlisberger D, Dym O, Albeck S, Houk KN, Baker D, Tawfik DS. Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Proceedings of the National Academy of Sciences of the United States of America. 109: 10358-63. PMID 22685214 DOI: 10.1073/Pnas.1121063109 |
0.438 |
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| 2012 |
Baxter S, Lambert AR, Kuhar R, Jarjour J, Kulshina N, Parmeggiani F, Danaher P, Gano J, Baker D, Stoddard BL, Scharenberg AM. Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases. Nucleic Acids Research. 40: 7985-8000. PMID 22684507 DOI: 10.1093/Nar/Gks502 |
0.318 |
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| 2012 |
Thompson JM, Sgourakis NG, Liu G, Rossi P, Tang Y, Mills JL, Szyperski T, Montelione GT, Baker D. Accurate protein structure modeling using sparse NMR data and homologous structure information. Proceedings of the National Academy of Sciences of the United States of America. 109: 9875-80. PMID 22665781 DOI: 10.1073/Pnas.1202485109 |
0.725 |
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| 2012 |
King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science (New York, N.Y.). 336: 1171-4. PMID 22654060 DOI: 10.1126/Science.1219364 |
0.736 |
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| 2012 |
Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H, Blair P, Wilson IA, Baker D. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nature Biotechnology. 30: 543-8. PMID 22634563 DOI: 10.1038/Nbt.2214 |
0.547 |
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| 2012 |
Fleishman SJ, Baker D. Role of the biomolecular energy gap in protein design, structure, and evolution. Cell. 149: 262-73. PMID 22500796 DOI: 10.1016/J.Cell.2012.03.016 |
0.41 |
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| 2012 |
Morin A, Urban J, Adams PD, Foster I, Sali A, Baker D, Sliz P. Research priorities. Shining light into black boxes. Science (New York, N.Y.). 336: 159-60. PMID 22499926 DOI: 10.1126/Science.1218263 |
0.51 |
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| 2012 |
Thyme SB, Baker D, Bradley P. Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. Journal of Molecular Biology. 419: 255-74. PMID 22426128 DOI: 10.1016/J.Jmb.2012.03.005 |
0.801 |
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| 2012 |
Lange OF, Baker D. Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins. 80: 884-95. PMID 22423358 DOI: 10.1002/Prot.23245 |
0.393 |
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| 2012 |
Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. Journal of Structural and Functional Genomics. 13: 81-90. PMID 22418934 DOI: 10.1007/S10969-012-9129-3 |
0.312 |
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| 2012 |
Althoff EA, Wang L, Jiang L, Giger L, Lassila JK, Wang Z, Smith M, Hari S, Kast P, Herschlag D, Hilvert D, Baker D. Robust design and optimization of retroaldol enzymes. Protein Science : a Publication of the Protein Society. 21: 717-26. PMID 22407837 DOI: 10.1002/Pro.2059 |
0.803 |
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| 2012 |
Krzysiak TC, Jung J, Thompson J, Baker D, Gronenborn AM. APOBEC2 is a monomer in solution: Implications for APOBEC3G Models Biochemistry. 51: 2008-2017. PMID 22339232 DOI: 10.1021/Bi300021S |
0.485 |
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| 2012 |
Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, et al. Blind testing of routine, fully automated determination of protein structures from NMR data. Structure (London, England : 1993). 20: 227-36. PMID 22325772 DOI: 10.1016/J.Str.2012.01.002 |
0.591 |
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| 2012 |
Khare SD, Kipnis Y, Greisen P, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature Chemical Biology. 8: 294-300. PMID 22306579 DOI: 10.1038/Nchembio.777 |
0.656 |
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| 2012 |
Wojdyla JA, Fleishman SJ, Baker D, Kleanthous C. Structure of the ultra-high-affinity colicin E2 DNase--Im2 complex. Journal of Molecular Biology. 417: 79-94. PMID 22306467 DOI: 10.1016/J.Jmb.2012.01.019 |
0.429 |
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| 2012 |
Schmitz C, Vernon R, Otting G, Baker D, Huber T. Protein structure determination from pseudocontact shifts using ROSETTA. Journal of Molecular Biology. 416: 668-77. PMID 22285518 DOI: 10.1016/J.Jmb.2011.12.056 |
0.567 |
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| 2012 |
Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CN, Kim PB, Cooper SR, Raisner RM, Herman A, Sivitz AB, Lakshmanaswamy A, Kashiyama Y, Baker D, Yoshikuni Y. An engineered microbial platform for direct biofuel production from brown macroalgae. Science (New York, N.Y.). 335: 308-13. PMID 22267807 DOI: 10.1126/Science.1214547 |
0.492 |
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| 2012 |
Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology. 30: 190-2. PMID 22267011 DOI: 10.1038/Nbt.2109 |
0.776 |
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| 2012 |
Yarov-Yarovoy V, DeCaen PG, Westenbroek RE, Pan CY, Scheuer T, Baker D, Catterall WA. Structural basis for gating charge movement in the voltage sensor of a sodium channel. Proceedings of the National Academy of Sciences of the United States of America. 109: E93-102. PMID 22160714 DOI: 10.1073/Pnas.1118434109 |
0.557 |
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| 2012 |
Handl J, Knowles J, Vernon R, Baker D, Lovell SC. The dual role of fragments in fragment-assembly methods for de novo protein structure prediction. Proteins. 80: 490-504. PMID 22095594 DOI: 10.1002/Prot.23215 |
0.602 |
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| 2012 |
Wang L, Althoff EA, Bolduc J, Jiang L, Moody J, Lassila JK, Giger L, Hilvert D, Stoddard B, Baker D. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. Journal of Molecular Biology. 415: 615-25. PMID 22075445 DOI: 10.1016/J.Jmb.2011.10.043 |
0.803 |
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| 2012 |
Azoitei ML, Ban YE, Julien JP, Bryson S, Schroeter A, Kalyuzhniy O, Porter JR, Adachi Y, Baker D, Pai EF, Schief WR. Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. Journal of Molecular Biology. 415: 175-92. PMID 22061265 DOI: 10.1016/J.Jmb.2011.10.003 |
0.352 |
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| 2012 |
Liu G, Koga N, Koga R, Xiao R, Hamilton K, Kohan E, Acton TB, Kornhaber G, Everett JK, Baker D, Montelione GT. Solution NMR Structure DE NOVO DESIGNED PFK fold PROTEIN, Northeast Structural Genomics Consortium (NESG) Target OR250 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Lvb/Pdb |
0.354 |
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| 2012 |
Liu G, Koga R, Koga N, Xiao R, Pederson K, Hamilton K, Kohan E, Acton T, Kornhaber G, Everett J, Baker D, Montelione G. SOLUTION NMR STRUCTURE OF DE NOVO DESIGNED PROTEIN, ROSSMANN 3x1 FOLD, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR157 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Lta/Pdb |
0.347 |
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| 2012 |
Brzovic P, Heikaus C, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P, Baker D, Klevit R, Hahn S. Structure of the complex of the central activation doamin of Gcn4 bound to the mediator co-activator domain 1 of Gal11/med15 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Lpb/Pdb |
0.519 |
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| 2012 |
Liu G, Koga N, Koga R, Xiao R, Lee H, Janjua H, Kohan E, Acton TB, Everett JK, Baker D, Montelione GT. Solution NMR Structure of DE NOVO DESIGNED PROTEIN, PFK fold, Northeast Structural Genomics Consortium Target OR134 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Lnd/Pdb |
0.354 |
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| 2012 |
Liu G, Koga R, Koga N, Xiao R, Lee H, Janjua H, Kohan E, Acton TB, Everett JK, Baker D, Montelione GT. Solution NMR Structure of DE NOVO DESIGNED PROTEIN, IF3-like fold, Northeast Structural Genomics Consortium Target OR135 (CASD target) Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Ln3/Pdb |
0.346 |
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| 2012 |
Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Erratum: Corrigendum: Atomic model of the type III secretion system needle Nature. 488: 684-684. DOI: 10.1038/Nature11350 |
0.652 |
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| 2012 |
Strauch E, Fleishman SJ, Baker D. De Novo Design of Protein Binders: Targeting Human IgG (Fc) Biophysical Journal. 102: 189a. DOI: 10.1016/J.Bpj.2011.11.1033 |
0.43 |
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| 2011 |
Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, Warfield L, Littlefield P, Baker D, Klevit RE, Hahn S. The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Molecular Cell. 44: 942-53. PMID 22195967 DOI: 10.1016/J.Molcel.2011.11.008 |
0.576 |
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| 2011 |
Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F, Thompson J, Baker D, Pichová I, Jaskolski M. High-resolution structure of a retroviral protease folded as a monomer. Acta Crystallographica. Section D, Biological Crystallography. 67: 907-14. PMID 22101816 DOI: 10.1107/S0907444911035943 |
0.757 |
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| 2011 |
Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popovic Z, Baker D, Players F. Algorithm discovery by protein folding game players. Proceedings of the National Academy of Sciences of the United States of America. 108: 18949-53. PMID 22065763 DOI: 10.1073/Pnas.1115898108 |
0.674 |
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| 2011 |
Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR. Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science (New York, N.Y.). 334: 373-6. PMID 22021856 DOI: 10.1126/Science.1209368 |
0.579 |
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| 2011 |
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... Baker D, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031 |
0.817 |
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| 2011 |
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Karanicolas J, Baker D. Hotspot-centric de novo design of protein binders. Journal of Molecular Biology. 413: 1047-62. PMID 21945116 DOI: 10.1016/J.Jmb.2011.09.001 |
0.817 |
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| 2011 |
Khatib F, DiMaio F, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popović Z, Jaskolski M, Baker D. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural & Molecular Biology. 18: 1175-7. PMID 21926992 DOI: 10.1038/Nsmb.2119 |
0.76 |
|
| 2011 |
Huang PS, Ban YE, Richter F, Andre I, Vernon R, Schief WR, Baker D. RosettaRemodel: a generalized framework for flexible backbone protein design. Plos One. 6: e24109. PMID 21909381 DOI: 10.1371/Journal.Pone.0024109 |
0.826 |
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| 2011 |
Gront D, Kulp DW, Vernon RM, Strauss CE, Baker D. Generalized fragment picking in Rosetta: design, protocols and applications. Plos One. 6: e23294. PMID 21887241 DOI: 10.1371/Journal.Pone.0023294 |
0.572 |
|
| 2011 |
Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW, Baker D, Kay LE. Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature. 477: 111-4. PMID 21857680 DOI: 10.1038/Nature10349 |
0.573 |
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| 2011 |
Wang RYR, Han Y, Krassovsky K, Sheffler W, Tyka M, Baker D. Modeling disordered regions in proteins using Rosetta Plos One. 6. PMID 21829444 DOI: 10.1371/Journal.Pone.0022060 |
0.721 |
|
| 2011 |
Szeto MD, Boissel SJ, Baker D, Thyme SB. Mining endonuclease cleavage determinants in genomic sequence data. The Journal of Biological Chemistry. 286: 32617-27. PMID 21778233 DOI: 10.1074/Jbc.M111.259572 |
0.776 |
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| 2011 |
Wu SJ, Eiben CB, Carra JH, Huang I, Zong D, Liu P, Wu CT, Nivala J, Dunbar J, Huber T, Senft J, Schokman R, Smith MD, Mills JH, Friedlander AM, Baker D, et al. Improvement of a potential anthrax therapeutic by computational protein design. The Journal of Biological Chemistry. 286: 32586-92. PMID 21768086 DOI: 10.1074/Jbc.M111.251041 |
0.788 |
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| 2011 |
DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I. Modeling symmetric macromolecular structures in Rosetta3. Plos One. 6: e20450. PMID 21731614 DOI: 10.1371/Journal.Pone.0020450 |
0.818 |
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| 2011 |
Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. Plos One. 6: e20161. PMID 21731610 DOI: 10.1371/Journal.Pone.0020161 |
0.813 |
|
| 2011 |
Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature. 475: 96-100. PMID 21677644 DOI: 10.1038/Nature10154 |
0.689 |
|
| 2011 |
Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE. Nonnative interactions in the FF domain folding pathway from an atomic resolution structure of a sparsely populated intermediate: an NMR relaxation dispersion study. Journal of the American Chemical Society. 133: 10974-82. PMID 21639149 DOI: 10.1021/Ja203686T |
0.568 |
|
| 2011 |
Thompson J, Baker D. Incorporation of evolutionary information into Rosetta comparative modeling. Proteins. 79: 2380-8. PMID 21638331 DOI: 10.1002/Prot.23046 |
0.558 |
|
| 2011 |
Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A. Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set. Journal of Molecular Biology. 411: 83-95. PMID 21624375 DOI: 10.1016/J.Jmb.2011.05.022 |
0.356 |
|
| 2011 |
Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D. De novo enzyme design using Rosetta3. Plos One. 6: e19230. PMID 21603656 DOI: 10.1371/Journal.Pone.0019230 |
0.797 |
|
| 2011 |
Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, Strauch EM, Wilson IA, Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (New York, N.Y.). 332: 816-21. PMID 21566186 DOI: 10.1126/Science.1202617 |
0.779 |
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| 2011 |
Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak LA, Baker D, Frydman J, Levitt M, Chiu W. Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. Structure (London, England : 1993). 19: 633-9. PMID 21565698 DOI: 10.1016/J.Str.2011.03.005 |
0.668 |
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| 2011 |
DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D. Improved molecular replacement by density- and energy-guided protein structure optimization. Nature. 473: 540-3. PMID 21532589 DOI: 10.1038/Nature09964 |
0.422 |
|
| 2011 |
Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D, Monnat RJ, Burt A, Crisanti A. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature. 473: 212-5. PMID 21508956 DOI: 10.1038/Nature09937 |
0.702 |
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| 2011 |
Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Structure-guided forcefield optimization. Proteins. 79: 1898-909. PMID 21488100 DOI: 10.1002/Prot.23013 |
0.776 |
|
| 2011 |
Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. Journal of the American Chemical Society. 133: 6288-98. PMID 21466200 DOI: 10.1021/Ja111318M |
0.803 |
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| 2011 |
Karanicolas J, Corn JE, Chen I, Joachimiak LA, Dym O, Peck SH, Albeck S, Unger T, Hu W, Liu G, Delbecq S, Montelione GT, Spiegel CP, Liu DR, Baker D. A de novo protein binding pair by computational design and directed evolution. Molecular Cell. 42: 250-60. PMID 21458342 DOI: 10.1016/J.Molcel.2011.03.010 |
0.812 |
|
| 2011 |
Fleishman SJ, Khare SD, Koga N, Baker D. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Science : a Publication of the Protein Society. 20: 753-7. PMID 21432939 DOI: 10.1002/Pro.604 |
0.629 |
|
| 2011 |
Kellogg EH, Leaver-Fay A, Baker D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins. 79: 830-8. PMID 21287615 DOI: 10.1002/Prot.22921 |
0.804 |
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| 2011 |
Khersonsky O, Röthlisberger D, Wollacott AM, Murphy P, Dym O, Albeck S, Kiss G, Houk KN, Baker D, Tawfik DS. Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution. Journal of Molecular Biology. 407: 391-412. PMID 21277311 DOI: 10.1016/J.Jmb.2011.01.041 |
0.806 |
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| 2011 |
Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W. Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proceedings of the National Academy of Sciences of the United States of America. 108: 1355-60. PMID 21220301 DOI: 10.1073/Pnas.1015739108 |
0.356 |
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| 2011 |
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, ... ... Baker D, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6 |
0.773 |
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| 2011 |
Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Alternate states of proteins revealed by detailed energy landscape mapping. Journal of Molecular Biology. 405: 607-18. PMID 21073878 DOI: 10.1016/J.Jmb.2010.11.008 |
0.594 |
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| 2011 |
Koga N, Koga(Tatsumi) R, Liu G, Xiao R, Montelione GT, Baker D. 1H1648 P22 Computational De Novo Design of Protein Structures(Protein: Property 2,The 49th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 51: S51. DOI: 10.2142/Biophys.51.S51_3 |
0.388 |
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| 2011 |
Koga N, Koga(Tatsumi) R, Liu G, Xiao R, Montelione GT, Baker D. 1SB-01 Computational De Novo Design of Protein Structures(1SB Exploring design principles of life,The 49th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 51: S2. DOI: 10.2142/Biophys.51.S2_1 |
0.385 |
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| 2011 |
Liu G, Koga N, Koga R, Xiao R, Janjua H, Ciccosanti c, Lee H, Acton T, Everett J, Baker D, Montelione G. Solution Nmr Structure Of De Novo Designed Protein, P-Loop Ntpase Fold, Northeast Structural Genomics Consortium Target Or136 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr17613 |
0.349 |
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| 2011 |
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, Clair JLS, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. A Biocatalytic Diels-Alder Reaction Using a DesignedEnzyme Synfacts. 2011: 323-323. DOI: 10.1055/S-0030-1259455 |
0.749 |
|
| 2011 |
Yarov-Yarovoy VM, DeCaen P, Scheuer T, Baker D, Catterall WA. High-Resolution Structural Modeling of Voltage-Dependent Conformational Changes in the Voltage Sensor of NaChBac Biophysical Journal. 100: 422a. DOI: 10.1016/J.Bpj.2010.12.2499 |
0.55 |
|
| 2010 |
Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, Bachovchin DA, Mowen K, Baker D, Cravatt BF. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature. 468: 790-5. PMID 21085121 DOI: 10.1038/Nature09472 |
0.787 |
|
| 2010 |
Liu L, Murphy P, Baker D, Lutz S. Computational design of orthogonal nucleoside kinases. Chemical Communications (Cambridge, England). 46: 8803-5. PMID 20959903 DOI: 10.1039/C0Cc02961K |
0.58 |
|
| 2010 |
Correia BE, Ban YE, Holmes MA, Xu H, Ellingson K, Kraft Z, Carrico C, Boni E, Sather DN, Zenobia C, Burke KY, Bradley-Hewitt T, Bruhn-Johannsen JF, Kalyuzhniy O, Baker D, et al. Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure (London, England : 1993). 18: 1116-26. PMID 20826338 DOI: 10.1016/J.Str.2010.06.010 |
0.301 |
|
| 2010 |
Sanowar S, Singh P, Pfuetzner RA, André I, Zheng H, Spreter T, Strynadka NC, Gonen T, Baker D, Goodlett DR, Miller SI. Interactions of the transmembrane polymeric rings of the Salmonella enterica serovar Typhimurium type III secretion system. Mbio. 1. PMID 20824104 DOI: 10.1128/Mbio.00158-10 |
0.314 |
|
| 2010 |
Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, ... ... Baker D, et al. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 78: 3056-62. PMID 20737437 DOI: 10.1002/Prot.22829 |
0.32 |
|
| 2010 |
Tang Y, Schneider WM, Shen Y, Raman S, Inouye M, Baker D, Roth MJ, Montelione GT. Fully automated high-quality NMR structure determination of small (2)H-enriched proteins. Journal of Structural and Functional Genomics. 11: 223-32. PMID 20734145 DOI: 10.1007/S10969-010-9095-6 |
0.609 |
|
| 2010 |
Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S. High-resolution mapping of protein sequence-function relationships. Nature Methods. 7: 741-6. PMID 20711194 DOI: 10.1038/Nmeth.1492 |
0.704 |
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| 2010 |
Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popovi? Z, Players F. Predicting protein structures with a multiplayer online game. Nature. 466: 756-60. PMID 20686574 DOI: 10.1038/Nature09304 |
0.797 |
|
| 2010 |
Smagghe BJ, Huang PS, Ban YE, Baker D, Springer TA. Modulation of integrin activation by an entropic spring in the {beta}-knee. The Journal of Biological Chemistry. 285: 32954-66. PMID 20670939 DOI: 10.1074/Jbc.M110.145177 |
0.51 |
|
| 2010 |
Kiss G, Röthlisberger D, Baker D, Houk KN. Evaluation and ranking of enzyme designs. Protein Science : a Publication of the Protein Society. 19: 1760-73. PMID 20665693 DOI: 10.1002/Pro.462 |
0.49 |
|
| 2010 |
Sheffler W, Baker D. RosettaHoles2: A volumetric packing measure for protein structure refinement and validation Protein Science. 19: 1991-1995. PMID 20665689 DOI: 10.1002/Pro.458 |
0.734 |
|
| 2010 |
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science (New York, N.Y.). 329: 309-13. PMID 20647463 DOI: 10.1126/Science.1190239 |
0.785 |
|
| 2010 |
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins. 78: 3212-8. PMID 20597089 DOI: 10.1002/Prot.22784 |
0.794 |
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| 2010 |
Meenan NA, Sharma A, Fleishman SJ, Macdonald CJ, Morel B, Boetzel R, Moore GR, Baker D, Kleanthous C. The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction. Proceedings of the National Academy of Sciences of the United States of America. 107: 10080-5. PMID 20479265 DOI: 10.1073/Pnas.0910756107 |
0.344 |
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| 2010 |
Zelter A, Hoopmann MR, Vernon R, Baker D, MacCoss MJ, Davis TN. Isotope signatures allow identification of chemically cross-linked peptides by mass spectrometry: A novel method to determine interresidue distances in protein structures through cross-linking Journal of Proteome Research. 9: 3583-3589. PMID 20476776 DOI: 10.1021/Pr1001115 |
0.587 |
|
| 2010 |
Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Research. 38: 5601-8. PMID 20435674 DOI: 10.1093/Nar/Gkq283 |
0.747 |
|
| 2010 |
Lassila JK, Baker D, Herschlag D. Origins of catalysis by computationally designed retroaldolase enzymes. Proceedings of the National Academy of Sciences of the United States of America. 107: 4937-42. PMID 20194782 DOI: 10.1073/Pnas.0913638107 |
0.542 |
|
| 2010 |
Das R, Karanicolas J, Baker D. Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods. 7: 291-4. PMID 20190761 DOI: 10.1038/Nmeth.1433 |
0.687 |
|
| 2010 |
Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D. NMR structure determination for larger proteins using backbone-only data. Science (New York, N.Y.). 327: 1014-8. PMID 20133520 DOI: 10.1126/Science.1183649 |
0.609 |
|
| 2010 |
Blum B, Jordan MI, Baker D. Feature space resampling for protein conformational search. Proteins. 78: 1583-93. PMID 20131376 DOI: 10.1002/Prot.22677 |
0.378 |
|
| 2010 |
Wang C, Vernon R, Lange O, Tyka M, Baker D. Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. Protein Science : a Publication of the Protein Society. 19: 494-506. PMID 20054832 DOI: 10.1002/Pro.327 |
0.702 |
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| 2010 |
Khersonsky O, Röthlisberger D, Dym O, Albeck S, Jackson CJ, Baker D, Tawfik DS. Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. Journal of Molecular Biology. 396: 1025-42. PMID 20036254 DOI: 10.1016/J.Jmb.2009.12.031 |
0.329 |
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| 2010 |
Raman S, Huang YJ, Mao B, Rossi P, Aramini JM, Liu G, Montelione GT, Baker D. Accurate automated protein NMR structure determination using unassigned NOESY data. Journal of the American Chemical Society. 132: 202-7. PMID 20000319 DOI: 10.1021/Ja905934C |
0.592 |
|
| 2010 |
Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A. De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds. Protein Science : a Publication of the Protein Society. 19: 349-56. PMID 19998407 DOI: 10.1002/Pro.303 |
0.56 |
|
| 2010 |
Leung CC, Kellogg E, Kuhnert A, Hänel F, Baker D, Glover JN. Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIbeta binding protein 1. Protein Science : a Publication of the Protein Society. 19: 162-7. PMID 19937654 DOI: 10.1002/Pro.290 |
0.691 |
|
| 2010 |
Koga N, Koga R, Baker D. 3P098 Computational de novo design of "ideal" protein structures(Protein: Engineering,The 48th Annual Meeting of the Biophysical Society of Japan) Biophysics. 50. DOI: 10.2142/Biophys.50.S162_1 |
0.356 |
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| 2009 |
Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. Exploitation of binding energy for catalysis and design. Nature. 461: 1300-4. PMID 19865174 DOI: 10.1038/Nature08508 |
0.793 |
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| 2009 |
Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 18978-83. PMID 19864631 DOI: 10.1073/Pnas.0904407106 |
0.729 |
|
| 2009 |
Afari N, Harder LH, Madra NJ, Heppner PS, Moeller-Bertram T, King C, Baker DG. PTSD, combat injury, and headache in Veterans Returning from Iraq/Afghanistan. Headache. 49: 1267-76. PMID 19788469 DOI: 10.1111/J.1526-4610.2009.01517.X |
0.386 |
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| 2009 |
Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins. 77: 114-22. PMID 19768677 DOI: 10.1002/Prot.22570 |
0.787 |
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| 2009 |
Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Montelione GT, et al. CASD-NMR: critical assessment of automated structure determination by NMR. Nature Methods. 6: 625-6. PMID 19718014 DOI: 10.1038/Nmeth0909-625 |
0.601 |
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| 2009 |
Kidd BA, Baker D, Thomas WE. Computation of conformational coupling in allosteric proteins. Plos Computational Biology. 5: e1000484. PMID 19714199 DOI: 10.1371/Journal.Pcbi.1000484 |
0.395 |
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| 2009 |
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77: 89-99. PMID 19701941 DOI: 10.1002/Prot.22540 |
0.811 |
|
| 2009 |
Kim DE, Blum B, Bradley P, Baker D. Sampling bottlenecks in de novo protein structure prediction. Journal of Molecular Biology. 393: 249-60. PMID 19646450 DOI: 10.1016/J.Jmb.2009.07.063 |
0.629 |
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| 2009 |
DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D. Refinement of protein structures into low-resolution density maps using rosetta. Journal of Molecular Biology. 392: 181-90. PMID 19596339 DOI: 10.1016/J.Jmb.2009.07.008 |
0.325 |
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| 2009 |
Davis IW, Raha K, Head MS, Baker D. Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Science : a Publication of the Protein Society. 18: 1998-2002. PMID 19554568 DOI: 10.1002/Pro.192 |
0.505 |
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| 2009 |
Havranek JJ, Baker D. Motif-directed flexible backbone design of functional interactions. Protein Science : a Publication of the Protein Society. 18: 1293-305. PMID 19472357 DOI: 10.1002/Pro.142 |
0.674 |
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| 2009 |
Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D. Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106: 9215-20. PMID 19470646 DOI: 10.1073/Pnas.0811070106 |
0.638 |
|
| 2009 |
Spreter T, Yip CK, Sanowar S, André I, Kimbrough TG, Vuckovic M, Pfuetzner RA, Deng W, Yu AC, Finlay BB, Baker D, Miller SI, Strynadka NC. A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nature Structural & Molecular Biology. 16: 468-76. PMID 19396170 DOI: 10.1038/Nsmb.1603 |
0.609 |
|
| 2009 |
Zhu J, Luo BH, Barth P, Schonbrun J, Baker D, Springer TA. The structure of a receptor with two associating transmembrane domains on the cell surface: integrin alphaIIbbeta3. Molecular Cell. 34: 234-49. PMID 19394300 DOI: 10.1016/J.Molcel.2009.02.022 |
0.553 |
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| 2009 |
Ashworth J, Baker D. Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Nucleic Acids Research. 37: e73. PMID 19389725 DOI: 10.1093/Nar/Gkp242 |
0.626 |
|
| 2009 |
Sadreyev RI, Shi S, Baker D, Grishin NV. Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics (Oxford, England). 25: 1259-63. PMID 19321733 DOI: 10.1093/Bioinformatics/Btp148 |
0.352 |
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| 2009 |
Dietrich JA, Yoshikuni Y, Fisher KJ, Woolard FX, Ockey D, McPhee DJ, Renninger NS, Chang MC, Baker D, Keasling JD. A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3). Acs Chemical Biology. 4: 261-7. PMID 19271725 DOI: 10.1021/Cb900006H |
0.518 |
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| 2009 |
Muratore KE, Seeliger MA, Wang Z, Fomina D, Neiswinger J, Havranek JJ, Baker D, Kuriyan J, Cole PA. Comparative analysis of mutant tyrosine kinase chemical rescue. Biochemistry. 48: 3378-86. PMID 19260709 DOI: 10.1021/Bi900057G |
0.608 |
|
| 2009 |
Barth P, Wallner B, Baker D. Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences of the United States of America. 106: 1409-14. PMID 19190187 DOI: 10.1073/Pnas.0808323106 |
0.732 |
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| 2009 |
Sheffler W, Baker D. RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation Protein Science. 18: 229-239. PMID 19177366 DOI: 10.1002/Pro.8 |
0.74 |
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| 2009 |
Das R, Baker D. Prospects for de novo phasing with de novo protein models. Acta Crystallographica. Section D, Biological Crystallography. 65: 169-75. PMID 19171972 DOI: 10.1107/S0907444908020039 |
0.55 |
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| 2009 |
Davis IW, Baker D. RosettaLigand docking with full ligand and receptor flexibility. Journal of Molecular Biology. 385: 381-92. PMID 19041878 DOI: 10.1016/J.Jmb.2008.11.010 |
0.507 |
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| 2009 |
Shen Y, Vernon R, Baker D, Bax A. De novo protein structure generation from incomplete chemical shift assignments. Journal of Biomolecular Nmr. 43: 63-78. PMID 19034676 DOI: 10.1007/S10858-008-9288-5 |
0.664 |
|
| 2009 |
Luo BH, Karanicolas J, Harmacek LD, Baker D, Springer TA. Rationally designed integrin beta3 mutants stabilized in the high affinity conformation. The Journal of Biological Chemistry. 284: 3917-24. PMID 19019827 DOI: 10.1074/Jbc.M806312200 |
0.637 |
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| 2009 |
Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA. Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins. 75: 147-67. PMID 18816799 DOI: 10.1002/Prot.22229 |
0.576 |
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| 2009 |
Liu G, Koga R, Koga N, Xiao R, Pederson K, Hamilton K, Ciccosanti C, Acton TB, Everett JK, Baker D, Montelione GT. Solution NMR Structure de novo designed rossmann 2x2 fold protein, Northeast Structural Genomics Consortium (NESG) Target OR16 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Kpo/Pdb |
0.347 |
|
| 2009 |
Liu G, Koga N, Jiang J, Xiao R, Ciccosanti C, Locke J, Everett J, Nair R, Acton T, Rost B, Baker D, Montelione G. Solution NMR Structure of denovo designed ferrodoxin fold like protein, Northeast Structural Genomics Consortium Target Target OR15 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr16387 |
0.345 |
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| 2008 |
Alexandrova AN, Röthlisberger D, Baker D, Jorgensen WL. Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination. Journal of the American Chemical Society. 130: 15907-15. PMID 18975945 DOI: 10.1021/Ja804040S |
0.327 |
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| 2008 |
André I, Strauss CE, Kaplan DB, Bradley P, Baker D. Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America. 105: 16148-52. PMID 18849473 DOI: 10.1073/Pnas.0807576105 |
0.715 |
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| 2008 |
Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL. A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell. 134: 1007-18. PMID 18805093 DOI: 10.1016/J.Cell.2008.07.042 |
0.628 |
|
| 2008 |
Fan E, Baker D, Fields S, Gelb MH, Buckner FS, Van Voorhis WC, Phizicky E, Dumont M, Mehlin C, Grayhack E, Sullivan M, Verlinde C, Detitta G, Meldrum DR, Merritt EA, et al. Structural genomics of pathogenic protozoa: an overview. Methods in Molecular Biology (Clifton, N.J.). 426: 497-513. PMID 18542886 DOI: 10.1007/978-1-60327-058-8_33 |
0.331 |
|
| 2008 |
Cho HD, Sood VD, Baker D, Weiner AM. On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes. Rna (New York, N.Y.). 14: 1284-9. PMID 18495940 DOI: 10.1261/Rna.1060308 |
0.567 |
|
| 2008 |
Keeble AH, Joachimiak LA, Maté MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C. Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. Journal of Molecular Biology. 379: 745-59. PMID 18471830 DOI: 10.1016/J.Jmb.2008.03.055 |
0.704 |
|
| 2008 |
Das R, Baker D. Macromolecular modeling with rosetta. Annual Review of Biochemistry. 77: 363-82. PMID 18410248 DOI: 10.1146/Annurev.Biochem.77.062906.171838 |
0.598 |
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| 2008 |
Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D. Kemp elimination catalysts by computational enzyme design. Nature. 453: 190-5. PMID 18354394 DOI: 10.1038/Nature06879 |
0.794 |
|
| 2008 |
Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, et al. Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America. 105: 4685-90. PMID 18326625 DOI: 10.1073/Pnas.0800256105 |
0.558 |
|
| 2008 |
Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF, Hilvert D, Houk KN, Stoddard BL, Baker D. De novo computational design of retro-aldol enzymes. Science (New York, N.Y.). 319: 1387-91. PMID 18323453 DOI: 10.1126/Science.1152692 |
0.813 |
|
| 2008 |
Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105: 4144-9. PMID 18322008 DOI: 10.1073/Pnas.0709032105 |
0.626 |
|
| 2008 |
McBeth C, Seamons A, Pizarro JC, Fleishman SJ, Baker D, Kortemme T, Goverman JM, Strong RK. A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Journal of Molecular Biology. 375: 1306-19. PMID 18155234 DOI: 10.1016/J.Jmb.2007.11.020 |
0.582 |
|
| 2008 |
Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support vector regression. Proteins. 71: 1175-82. PMID 18004754 DOI: 10.1002/Prot.21809 |
0.718 |
|
| 2008 |
Koga N, Tatsumi-Koga R, Baker D. 2P-097 De novo computational design of "ideal" protein structure(The 46th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 48. DOI: 10.2142/Biophys.48.S90_2 |
0.351 |
|
| 2008 |
Raman S, Qian B, Baker D, Walker RC. Advances in Rosetta protein structure prediction on massively parallel systems Ibm Journal of Research and Development. 52: 7-18. DOI: 10.1147/Rd.521.0007 |
0.634 |
|
| 2007 |
Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler-Furman O, Popham JM, Baker D, Campbell CT, Stayton PS, Drobny GP. The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. Magnetic Resonance in Chemistry : Mrc. 45: S32-47. PMID 18172904 DOI: 10.1002/Mrc.2123 |
0.627 |
|
| 2007 |
André I, Bradley P, Wang C, Baker D. Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104: 17656-61. PMID 17978193 DOI: 10.1073/Pnas.0702626104 |
0.793 |
|
| 2007 |
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature. 450: 259-64. PMID 17934447 DOI: 10.1038/Nature06249 |
0.763 |
|
| 2007 |
Barth P, Schonbrun J, Baker D. Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 15682-7. PMID 17905872 DOI: 10.1073/Pnas.0702515104 |
0.646 |
|
| 2007 |
Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, ... Baker D, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/Prot.21636 |
0.798 |
|
| 2007 |
Wojtowicz WM, Wu W, Andre I, Qian B, Baker D, Zipursky SL. A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains. Cell. 130: 1134-45. PMID 17889655 DOI: 10.1016/J.Cell.2007.08.026 |
0.617 |
|
| 2007 |
Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. Journal of Molecular Biology. 373: 503-19. PMID 17825317 DOI: 10.1016/J.Jmb.2007.07.050 |
0.716 |
|
| 2007 |
Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 14664-9. PMID 17726102 DOI: 10.1073/Pnas.0703836104 |
0.547 |
|
| 2007 |
Lengyel CS, Willis LJ, Mann P, Baker D, Kortemme T, Strong RK, McFarland BJ. Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity. The Journal of Biological Chemistry. 282: 30658-66. PMID 17690100 DOI: 10.1074/Jbc.M704513200 |
0.601 |
|
| 2007 |
Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69: 137-51. PMID 17680686 DOI: 10.1002/Prot.21675 |
0.681 |
|
| 2007 |
Wang C, Schueler-Furman O, Andre I, London N, Fleishman SJ, Bradley P, Qian B, Baker D. RosettaDock in CAPRI rounds 6-12. Proteins. 69: 758-63. PMID 17671979 DOI: 10.1002/Prot.21684 |
0.818 |
|
| 2007 |
Stankunas K, Bayle JH, Havranek JJ, Wandless TJ, Baker D, Crabtree GR, Gestwicki JE. Rescue of degradation-prone mutants of the FK506-rapamycin binding (FRB) protein with chemical ligands. Chembiochem : a European Journal of Chemical Biology. 8: 1162-9. PMID 17525916 DOI: 10.1002/Cbic.200700087 |
0.616 |
|
| 2007 |
Malmström L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology Plos Biology. 5. PMID 17373854 DOI: 10.1371/Journal.Pbio.0050076 |
0.793 |
|
| 2007 |
Yatsenko AS, Gray EE, Shcherbata HR, Patterson LB, Sood VD, Kucherenko MM, Baker D, Ruohola-Baker H. A putative Src homology 3 domain binding motif but not the C-terminal dystrophin WW domain binding motif is required for dystroglycan function in cellular polarity in Drosophila. The Journal of Biological Chemistry. 282: 15159-69. PMID 17355978 DOI: 10.1074/Jbc.M608800200 |
0.56 |
|
| 2007 |
Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, Baker D. The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell. 128: 613-24. PMID 17289578 DOI: 10.1016/J.Cell.2006.12.042 |
0.771 |
|
| 2007 |
Shcherbata HR, Yatsenko AS, Patterson L, Sood VD, Nudel U, Yaffe D, Baker D, Ruohola-Baker H. Dissecting muscle and neuronal disorders in a Drosophila model of muscular dystrophy. The Embo Journal. 26: 481-93. PMID 17215867 DOI: 10.1038/Sj.Emboj.7601503 |
0.511 |
|
| 2007 |
Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. Journal of Molecular Biology. 366: 1209-21. PMID 17196978 DOI: 10.1016/J.Jmb.2006.11.080 |
0.806 |
|
| 2007 |
Wollacott AM, Zanghellini A, Murphy P, Baker D. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Science : a Publication of the Protein Society. 16: 165-75. PMID 17189483 DOI: 10.1110/Ps.062270707 |
0.803 |
|
| 2006 |
Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, Althoff EA, Röthlisberger D, Baker D. New algorithms and an in silico benchmark for computational enzyme design. Protein Science : a Publication of the Protein Society. 15: 2785-94. PMID 17132862 DOI: 10.1110/Ps.062353106 |
0.793 |
|
| 2006 |
Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W. Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. Plos Computational Biology. 2: e146. PMID 17069457 DOI: 10.1371/Journal.Pcbi.0020146 |
0.728 |
|
| 2006 |
Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP. Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences of the United States of America. 103: 16083-8. PMID 17060618 DOI: 10.1073/Pnas.0607193103 |
0.614 |
|
| 2006 |
Bradley P, Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins. 65: 922-9. PMID 17034045 DOI: 10.1002/Prot.21133 |
0.573 |
|
| 2006 |
Meiler J, Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins. 65: 538-48. PMID 16972285 DOI: 10.1002/Prot.21086 |
0.566 |
|
| 2006 |
Chivian D, Baker D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection Nucleic Acids Research. 34. PMID 16971460 DOI: 10.1093/Nar/Gkl480 |
0.737 |
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