| Year |
Citation |
Score |
| 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 |
0.3 |
|
| 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 |
0.33 |
|
| 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 |
0.323 |
|
| 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 |
0.324 |
|
| 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 |
0.364 |
|
| 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 |
0.301 |
|
| 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 |
0.356 |
|
| 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 |
0.336 |
|
| 2020 |
Wu HQ, Baker D, Ovaa H. Small molecules that target the ubiquitin system. Biochemical Society Transactions. PMID 32196552 DOI: 10.1042/Bst20190535 |
0.3 |
|
| 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 |
0.356 |
|
| 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 |
0.332 |
|
| 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 |
0.324 |
|
| 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 |
0.355 |
|
| 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 |
0.354 |
|
| 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 |
0.378 |
|
| 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 |
0.343 |
|
| 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 |
0.356 |
|
| 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 |
0.324 |
|
| 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 |
0.329 |
|
| 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 |
0.343 |
|
| 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 |
0.356 |
|
| 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 |
0.372 |
|
| 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 |
0.316 |
|
| 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 |
0.309 |
|
| 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 |
0.327 |
|
| 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 |
0.358 |
|
| 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 |
0.335 |
|
| 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 |
0.311 |
|
| 2019 |
Baker D. Computationally designed protein activation National Science Review. 6: 609-610. DOI: 10.1093/Nsr/Nwz063 |
0.321 |
|
| 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 |
0.324 |
|
| 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 |
0.315 |
|
| 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 |
0.336 |
|
| 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 |
0.323 |
|
| 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 |
0.339 |
|
| 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 |
0.362 |
|
| 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 |
0.308 |
|
| 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 |
0.322 |
|
| 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 |
0.374 |
|
| 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 |
0.361 |
|
| 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 |
0.316 |
|
| 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 |
0.3 |
|
| 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 |
0.313 |
|
| 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 |
0.333 |
|
| 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 |
0.381 |
|
| 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 |
0.349 |
|
| 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 |
0.34 |
|
| 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 |
0.303 |
|
| 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 |
0.312 |
|
| 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 |
0.366 |
|
| 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 |
0.33 |
|
| 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 |
0.318 |
|
| 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 |
0.349 |
|
| 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 |
0.367 |
|
| 2017 |
Baker D, Pryce G, Visintin C, Sisay S, Bondarenko AI, Ho WSV, Jackson SJ, Williams TE, Al-Izki S, Sevastou I, Okuyama M, Graier WF, Stevenson LA, Tanner C, Ross R, et al. Big conductance calcium-activated potassium channel openers control spasticity without sedation. British Journal of Pharmacology. PMID 28677901 DOI: 10.1111/Bph.13889 |
0.382 |
|
| 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 |
0.315 |
|
| 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 |
0.316 |
|
| 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 |
0.322 |
|
| 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 |
0.353 |
|
| 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 |
0.315 |
|
| 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 |
0.327 |
|
| 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 |
0.312 |
|
| 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 |
0.325 |
|
| 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 |
0.368 |
|
| 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 |
0.303 |
|
| 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 |
0.326 |
|
| 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 |
0.329 |
|
| 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 |
0.33 |
|
| 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 |
0.305 |
|
| 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 |
0.344 |
|
| 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 |
0.303 |
|
| 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 |
0.361 |
|
| 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 |
0.317 |
|
| 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 |
0.349 |
|
| 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 |
0.312 |
|
| 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 |
0.312 |
|
| 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 |
0.316 |
|
| 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 |
0.323 |
|
| 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 |
0.329 |
|
| 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 |
0.327 |
|
| 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 |
0.323 |
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| 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 |
0.327 |
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| 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 |
0.383 |
|
| 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 |
0.385 |
|
| 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 |
0.308 |
|
| 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 |
0.352 |
|
| 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 |
0.323 |
|
| 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 |
0.335 |
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| 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 |
0.329 |
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| 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 |
0.363 |
|
| 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 |
0.353 |
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| 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 |
0.321 |
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| 2015 |
Park H, DiMaio F, Baker D. CASP11 refinement experiments with ROSETTA. Proteins. PMID 26205421 DOI: 10.1002/Prot.24862 |
0.33 |
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| 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 |
0.345 |
|
| 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 |
0.362 |
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| 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 |
0.362 |
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| 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 |
0.333 |
|
| 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 |
0.359 |
|
| 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 |
0.322 |
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| 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 |
0.365 |
|
| 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 |
0.337 |
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| 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 |
0.366 |
|
| 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 |
0.334 |
|
| 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 |
0.351 |
|
| 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 |
0.363 |
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| 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 |
0.365 |
|
| 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 |
0.351 |
|
| 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 |
0.303 |
|
| 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 |
0.349 |
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| 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 |
0.336 |
|
| 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 |
0.346 |
|
| 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 |
0.343 |
|
| 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 |
0.318 |
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| 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 |
0.348 |
|
| 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 |
0.377 |
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| 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 |
0.307 |
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| 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 |
0.341 |
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| 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 |
0.357 |
|
| 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 |
0.329 |
|
| 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 |
0.356 |
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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 |
0.393 |
|
| 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 |
0.344 |
|
| 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 |
0.333 |
|
| 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 |
0.305 |
|
| 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 |
0.357 |
|
| 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 |
0.311 |
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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 |
0.333 |
|
| 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 |
0.338 |
|
| 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 |
0.34 |
|
| 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 |
0.33 |
|
| 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 |
0.343 |
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| 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 |
0.343 |
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| 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 |
0.326 |
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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 |
0.347 |
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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 |
0.326 |
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| 2013 |
Lidster K, Jackson SJ, Ahmed Z, Munro P, Coffey P, Giovannoni G, Baker MD, Baker D. Neuroprotection in a novel mouse model of multiple sclerosis. Plos One. 8: e79188. PMID 24223903 DOI: 10.1371/Journal.Pone.0079188 |
0.413 |
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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 |
0.331 |
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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 |
0.345 |
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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 |
0.309 |
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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 |
0.34 |
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| 2013 |
Delarasse C, Smith P, Baker D, Amor S. Novel pathogenic epitopes of myelin oligodendrocyte glycoprotein induce experimental autoimmune encephalomyelitis in C57BL/6 mice Immunology. 140: 456-464. PMID 23876060 DOI: 10.1111/Imm.12155 |
0.301 |
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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 |
0.361 |
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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 |
0.319 |
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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 |
0.344 |
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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 |
0.316 |
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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 |
0.326 |
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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 |
0.375 |
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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 |
0.325 |
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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 |
0.34 |
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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 |
0.324 |
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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 |
0.314 |
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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 |
0.349 |
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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 |
0.325 |
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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 |
0.397 |
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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 |
0.316 |
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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 |
0.318 |
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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 |
0.322 |
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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 |
0.333 |
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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 |
0.331 |
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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 |
0.375 |
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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 |
0.327 |
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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 |
0.347 |
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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 |
0.341 |
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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 |
0.337 |
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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 |
0.305 |
|
| 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 |
0.352 |
|
| 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 |
0.37 |
|
| 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 |
0.317 |
|
| 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 |
0.305 |
|
| 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 |
0.357 |
|
| 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 |
0.308 |
|
| 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 |
0.307 |
|
| 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 |
0.35 |
|
| 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 |
0.342 |
|
| 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 |
0.35 |
|
| 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 |
0.34 |
|
| 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 |
0.365 |
|
| 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 |
0.322 |
|
| 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 |
0.364 |
|
| 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 |
0.343 |
|
| 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 |
0.367 |
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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 |
0.337 |
|
| 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 |
0.352 |
|
| 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 |
0.348 |
|
| 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 |
0.316 |
|
| 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 |
0.319 |
|
| 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 |
0.306 |
|
| 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 |
0.354 |
|
| 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 |
0.34 |
|
| 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 |
0.31 |
|
| 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 |
0.315 |
|
| 2011 |
Thompson J, Baker D. Incorporation of evolutionary information into Rosetta comparative modeling. Proteins. 79: 2380-8. PMID 21638331 DOI: 10.1002/Prot.23046 |
0.376 |
|
| 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 |
0.316 |
|
| 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 |
0.326 |
|
| 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 |
0.374 |
|
| 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 |
0.349 |
|
| 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 |
0.369 |
|
| 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 |
0.357 |
|
| 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 |
0.346 |
|
| 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 |
0.491 |
|
| 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 |
0.353 |
|
| 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 |
0.34 |
|
| 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 |
0.322 |
|
| 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 |
0.348 |
|
| 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 |
0.341 |
|
| 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 |
0.339 |
|
| 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 |
0.328 |
|
| 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 |
0.31 |
|
| 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 |
0.339 |
|
| 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 |
0.301 |
|
| 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 |
0.348 |
|
| 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 |
0.342 |
|
| 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 |
0.32 |
|
| 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 |
0.352 |
|
| 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 |
0.336 |
|
| 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 |
0.357 |
|
| 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 |
0.314 |
|
| 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 |
0.359 |
|
| 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 |
0.301 |
|
| 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 |
0.338 |
|
| 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 |
0.338 |
|
| 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 |
0.332 |
|
| 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 |
0.324 |
|
| 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 |
0.338 |
|
| 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 |
0.339 |
|
| 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 |
0.37 |
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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 |
0.443 |
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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 |
0.348 |
|
| 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 |
0.343 |
|
| 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 |
0.328 |
|
| 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 |
0.318 |
|
| 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 |
0.38 |
|
| 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 |
0.365 |
|
| 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 |
0.318 |
|
| 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 |
0.301 |
|
| 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 |
0.342 |
|
| 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 |
0.317 |
|
| 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 |
0.342 |
|
| 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 |
0.339 |
|
| 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 |
0.339 |
|
| 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 |
0.368 |
|
| 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 |
0.346 |
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| 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 |
0.328 |
|
| 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 |
0.323 |
|
| 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 |
0.33 |
|
| 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 |
0.377 |
|
| 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 |
0.311 |
|
| 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 |
0.364 |
|
| 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 |
0.341 |
|
| 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 |
0.37 |
|
| 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 |
0.332 |
|
| 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 |
0.357 |
|
| 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 |
0.306 |
|
| 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 |
0.37 |
|
| 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 |
0.304 |
|
| 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 |
0.34 |
|
| 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 |
0.349 |
|
| 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 |
0.379 |
|
| 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 |
0.36 |
|
| 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 |
0.499 |
|
| 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 |
0.301 |
|
| 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 |
0.352 |
|
| 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 |
0.338 |
|
| 2006 |
Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of Molecular Biology. 362: 1004-24. PMID 16949611 DOI: 10.1016/J.Jmb.2006.07.092 |
0.39 |
|
| 2006 |
Joachimiak LA, Kortemme T, Stoddard BL, Baker D. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. Journal of Molecular Biology. 361: 195-208. PMID 16831445 DOI: 10.1016/J.Jmb.2006.05.022 |
0.352 |
|
| 2006 |
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441: 656-9. PMID 16738662 DOI: 10.1038/Nature04818 |
0.33 |
|
| 2006 |
Dobson N, Dantas G, Baker D, Varani G. High-resolution structural validation of the computational redesign of human U1A protein. Structure (London, England : 1993). 14: 847-56. PMID 16698546 DOI: 10.1016/J.Str.2006.02.011 |
0.383 |
|
| 2006 |
Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America. 103: 5361-6. PMID 16567638 DOI: 10.1073/Pnas.0509355103 |
0.323 |
|
| 2006 |
Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103: 4074-8. PMID 16537487 DOI: 10.1073/Pnas.0511295103 |
0.304 |
|
| 2006 |
Baker D. Prediction and design of macromolecular structures and interactions. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 459-63. PMID 16524834 DOI: 10.1098/Rstb.2005.1803 |
0.332 |
|
| 2006 |
Arakaki T, Le Trong I, Phizicky E, Quartley E, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Worthey E, Myler PJ, Kim D, Baker D, Hol WG, Merritt EA. Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62: 175-9. PMID 16511295 DOI: 10.1107/S1744309106005902 |
0.352 |
|
| 2006 |
Sood VD, Baker D. Recapitulation and design of protein binding peptide structures and sequences. Journal of Molecular Biology. 357: 917-27. PMID 16473368 DOI: 10.1016/J.Jmb.2006.01.045 |
0.303 |
|
| 2006 |
Yarov-Yarovoy V, Schonbrun J, Baker D. Multipass membrane protein structure prediction using Rosetta. Proteins. 62: 1010-25. PMID 16372357 DOI: 10.1002/Prot.20817 |
0.338 |
|
| 2005 |
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science (New York, N.Y.). 310: 638-42. PMID 16254179 DOI: 10.1126/Science.1112160 |
0.349 |
|
| 2005 |
Lacy DB, Lin HC, Melnyk RA, Schueler-Furman O, Reither L, Cunningham K, Baker D, Collier RJ. A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America. 102: 16409-14. PMID 16251269 DOI: 10.1073/Pnas.0508259102 |
0.322 |
|
| 2005 |
Cheng G, Qian B, Samudrala R, Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research. 33: 5861-7. PMID 16224101 DOI: 10.1093/Nar/Gki894 |
0.355 |
|
| 2005 |
Kim DE, Chivian D, Malmström L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61: 193-200. PMID 16187362 DOI: 10.1002/Prot.20737 |
0.317 |
|
| 2005 |
Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D. Free modeling with Rosetta in CASP6. Proteins. 61: 128-34. PMID 16187354 DOI: 10.1002/Prot.20729 |
0.328 |
|
| 2005 |
Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science (New York, N.Y.). 309: 1868-71. PMID 16166519 DOI: 10.1126/Science.1113801 |
0.344 |
|
| 2005 |
Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins. 60: 187-94. PMID 15981249 DOI: 10.1002/Prot.20556 |
0.33 |
|
| 2005 |
Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Science : a Publication of the Protein Society. 14: 1328-39. PMID 15802647 DOI: 10.1110/Ps.041222905 |
0.351 |
|
| 2005 |
Meiler J, Baker D. The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 173: 310-6. PMID 15780923 DOI: 10.1016/J.Jmr.2004.11.031 |
0.363 |
|
| 2005 |
Misura KM, Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins. 59: 15-29. PMID 15690346 DOI: 10.1002/Prot.20376 |
0.365 |
|
| 2005 |
Saunders CT, Baker D. Recapitulation of protein family divergence using flexible backbone protein design. Journal of Molecular Biology. 346: 631-44. PMID 15670610 DOI: 10.1016/J.Jmb.2004.11.062 |
0.346 |
|
| 2005 |
Jiang L, Kuhlman B, Kortemme T, Baker D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58: 893-904. PMID 15651050 DOI: 10.1002/Prot.20347 |
0.344 |
|
| 2004 |
Havranek JJ, Duarte CM, Baker D. A simple physical model for the prediction and design of protein-DNA interactions. Journal of Molecular Biology. 344: 59-70. PMID 15504402 DOI: 10.1016/J.Jmb.2004.09.029 |
0.353 |
|
| 2004 |
Chen Y, Kortemme T, Robertson T, Baker D, Varani G. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Research. 32: 5147-62. PMID 15459285 DOI: 10.1093/Nar/Gkh785 |
0.307 |
|
| 2004 |
Misura KM, Morozov AV, Baker D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of Molecular Biology. 342: 651-64. PMID 15327962 DOI: 10.1016/J.Jmb.2004.07.038 |
0.366 |
|
| 2004 |
Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research. 32: W526-31. PMID 15215442 DOI: 10.1093/Nar/Gkh468 |
0.393 |
|
| 2004 |
Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Science : a Publication of the Protein Society. 13: 1660-9. PMID 15133165 DOI: 10.1110/Ps.03517304 |
0.326 |
|
| 2004 |
Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 55: 656-77. PMID 15103629 DOI: 10.1002/Prot.10629 |
0.38 |
|
| 2004 |
Kuhlman B, Baker D. Exploring folding free energy landscapes using computational protein design. Current Opinion in Structural Biology. 14: 89-95. PMID 15102454 DOI: 10.1016/J.Sbi.2004.01.002 |
0.371 |
|
| 2004 |
Watters AL, Baker D. Searching for folded proteins in vitro and in silico. European Journal of Biochemistry / Febs. 271: 1615-22. PMID 15096200 DOI: 10.1111/J.1432-1033.2004.04072.X |
0.364 |
|
| 2004 |
Scalley-Kim M, Baker D. Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. Journal of Molecular Biology. 338: 573-83. PMID 15081814 DOI: 10.1016/J.Jmb.2004.02.055 |
0.343 |
|
| 2004 |
Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods in Enzymology. 383: 66-93. PMID 15063647 DOI: 10.1016/S0076-6879(04)83004-0 |
0.36 |
|
| 2004 |
Kortemme T, Baker D. Computational design of protein-protein interactions. Current Opinion in Chemical Biology. 8: 91-7. PMID 15036162 DOI: 10.1016/J.Cbpa.2003.12.008 |
0.353 |
|
| 2004 |
Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. Computational redesign of protein-protein interaction specificity. Nature Structural & Molecular Biology. 11: 371-9. PMID 15034550 DOI: 10.1038/Nsmb749 |
0.355 |
|
| 2004 |
Ginalski K, Rychlewski L, Baker D, Grishin NV. Protein structure prediction for the male-specific region of the human Y chromosome. Proceedings of the National Academy of Sciences of the United States of America. 101: 2305-10. PMID 14983005 DOI: 10.1073/Pnas.0306306101 |
0.352 |
|
| 2004 |
Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Science's Stke : Signal Transduction Knowledge Environment. 2004: pl2. PMID 14872095 DOI: 10.1126/Stke.2192004Pl2 |
0.354 |
|
| 2004 |
Kuhn M, Meiler J, Baker D. Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54: 282-8. PMID 14696190 DOI: 10.1002/Prot.10589 |
0.31 |
|
| 2003 |
Hazbun TR, Malmström L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, et al. Assigning function to yeast proteins by integration of technologies. Molecular Cell. 12: 1353-65. PMID 14690591 DOI: 10.1016/S1097-2765(03)00476-3 |
0.347 |
|
| 2003 |
Meiler J, Baker D. Rapid protein fold determination using unassigned NMR data. Proceedings of the National Academy of Sciences of the United States of America. 100: 15404-9. PMID 14668443 DOI: 10.1073/Pnas.2434121100 |
0.346 |
|
| 2003 |
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science (New York, N.Y.). 302: 1364-8. PMID 14631033 DOI: 10.1126/Science.1089427 |
0.376 |
|
| 2003 |
Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53: 524-33. PMID 14579342 DOI: 10.1002/Prot.10529 |
0.345 |
|
| 2003 |
Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 53: 457-68. PMID 14579334 DOI: 10.1002/Prot.10552 |
0.366 |
|
| 2003 |
Meiler J, Baker D. Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences of the United States of America. 100: 12105-10. PMID 14528006 DOI: 10.1073/Pnas.1831973100 |
0.321 |
|
| 2003 |
Wedemeyer WJ, Baker D. Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates. Proteins. 53: 262-72. PMID 14517977 DOI: 10.1002/Prot.10525 |
0.312 |
|
| 2003 |
Sadreyev RI, Baker D, Grishin NV. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Science : a Publication of the Protein Society. 12: 2262-72. PMID 14500884 DOI: 10.1110/Ps.03197403 |
0.337 |
|
| 2003 |
Dantas G, Kuhlman B, Callender D, Wong M, Baker D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. Journal of Molecular Biology. 332: 449-60. PMID 12948494 DOI: 10.1016/S0022-2836(03)00888-X |
0.375 |
|
| 2003 |
Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53: 76-87. PMID 12945051 DOI: 10.1002/Prot.10454 |
0.361 |
|
| 2003 |
Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV. Contact order revisited: influence of protein size on the folding rate. Protein Science : a Publication of the Protein Society. 12: 2057-62. PMID 12931003 DOI: 10.1110/Ps.0302503 |
0.337 |
|
| 2003 |
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology. 331: 281-99. PMID 12875852 DOI: 10.1016/S0022-2836(03)00670-3 |
0.377 |
|
| 2003 |
Kinch LN, Baker D, Grishin NV. Deciphering a novel thioredoxin-like fold family. Proteins. 52: 323-31. PMID 12866046 DOI: 10.1002/Prot.10425 |
0.355 |
|
| 2003 |
Schueler-Furman O, Baker D. Conserved residue clustering and protein structure prediction. Proteins. 52: 225-35. PMID 12833546 DOI: 10.1002/Prot.10365 |
0.355 |
|
| 2003 |
Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins. 52: 118-22. PMID 12784377 DOI: 10.1002/Prot.10384 |
0.338 |
|
| 2003 |
Petzold A, Baker D, Pryce G, Keir G, Thompson EJ, Giovannoni G. Quantification of neurodegeneration by measurement of brain-specific proteins. Journal of Neuroimmunology. 138: 45-8. PMID 12742652 DOI: 10.1016/S0165-5728(03)00092-4 |
0.303 |
|
| 2003 |
Chivian D, Robertson T, Bonneau R, Baker D. Ab initio methods Methods of Biochemical Analysis. 44: 547-557. PMID 12647404 DOI: 10.1002/0471721204.Ch27 |
0.322 |
|
| 2003 |
Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. Journal of Molecular Biology. 326: 1239-59. PMID 12589766 DOI: 10.1016/S0022-2836(03)00021-4 |
0.351 |
|
| 2003 |
Scalley-Kim M, Minard P, Baker D. Low free energy cost of very long loop insertions in proteins. Protein Science : a Publication of the Protein Society. 12: 197-206. PMID 12538883 DOI: 10.1110/Ps.0232003 |
0.312 |
|
| 2002 |
Baker D. Progress in AB Initio Protein Structure Prediction. The Scientific World Journal. 2: 31-31. PMID 29973789 DOI: 10.1100/Tsw.2002.15 |
0.373 |
|
| 2002 |
Nauli S, Kuhlman B, Le Trong I, Stenkamp RE, Teller D, Baker D. Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein Science : a Publication of the Protein Society. 11: 2924-31. PMID 12441390 DOI: 10.1110/Ps.0216902 |
0.351 |
|
| 2002 |
Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. Design, activity, and structure of a highly specific artificial endonuclease. Molecular Cell. 10: 895-905. PMID 12419232 DOI: 10.1016/S1097-2765(02)00690-1 |
0.351 |
|
| 2002 |
Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 99: 14116-21. PMID 12381794 DOI: 10.1073/Pnas.202485799 |
0.361 |
|
| 2002 |
Saunders CT, Baker D. Evaluation of structural and evolutionary contributions to deleterious mutation prediction. Journal of Molecular Biology. 322: 891-901. PMID 12270722 DOI: 10.1016/S0022-2836(02)00813-6 |
0.308 |
|
| 2002 |
Alm E, Morozov AV, Kortemme T, Baker D. Simple physical models connect theory and experiment in protein folding kinetics. Journal of Molecular Biology. 322: 463-76. PMID 12217703 DOI: 10.1016/S0022-2836(02)00706-4 |
0.344 |
|
| 2002 |
Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. Journal of Molecular Biology. 322: 65-78. PMID 12215415 DOI: 10.1016/S0022-2836(02)00698-8 |
0.382 |
|
| 2002 |
Bonneau R, Ruczinski I, Tsai J, Baker D. Contact order and ab initio protein structure prediction. Protein Science : a Publication of the Protein Society. 11: 1937-44. PMID 12142448 DOI: 10.1110/Ps.3790102 |
0.373 |
|
| 2002 |
Schonbrun J, Wedemeyer WJ, Baker D. Protein structure prediction in 2002. Current Opinion in Structural Biology. 12: 348-54. PMID 12127454 DOI: 10.1016/S0959-440X(02)00336-6 |
0.344 |
|
| 2002 |
Ruczinski I, Kooperberg C, Bonneau R, Baker D. Distributions of beta sheets in proteins with application to structure prediction Proteins: Structure, Function and Genetics. 48: 85-97. PMID 12012340 DOI: 10.1002/Prot.10123 |
0.337 |
|
| 2002 |
Krantz BA, Srivastava AK, Nauli S, Baker D, Sauer RT, Sosnick TR. Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature Structural Biology. 9: 458-63. PMID 11979278 DOI: 10.1038/Nsb794 |
0.301 |
|
| 2002 |
Walters CE, Pryce G, Hankey DJ, Sebti SM, Hamilton AD, Baker D, Greenwood J, Adamson P. Inhibition of Rho GTPases with protein prenyltransferase inhibitors prevents leukocyte recruitment to the central nervous system and attenuates clinical signs of disease in an animal model of multiple sclerosis. Journal of Immunology (Baltimore, Md. : 1950). 168: 4087-94. PMID 11937568 DOI: 10.4049/Jimmunol.168.8.4087 |
0.322 |
|
| 2002 |
Rohl CA, Baker D. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. Journal of the American Chemical Society. 124: 2723-9. PMID 11890823 DOI: 10.1021/Ja016880E |
0.367 |
|
| 2002 |
Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW. Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. Journal of Molecular Biology. 316: 225-33. PMID 11851333 DOI: 10.1006/Jmbi.2001.5344 |
0.341 |
|
| 2002 |
Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of Molecular Biology. 315: 471-7. PMID 11786026 DOI: 10.1006/Jmbi.2001.5229 |
0.349 |
|
| 2001 |
Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. 119-26. PMID 11835488 DOI: 10.1002/Prot.1170 |
0.369 |
|
| 2001 |
Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction. Journal of Molecular Biology. 313: 417-30. PMID 11800566 DOI: 10.1006/Jmbi.2001.5032 |
0.342 |
|
| 2001 |
Baker D, Sali A. Protein Structure Prediction and Structural Genomics Science. 294: 93-96. PMID 11588250 DOI: 10.1126/Science.1065659 |
0.37 |
|
| 2001 |
Bonneau R, Tsai J, Ruczinski I, Baker D. Functional inferences from blind ab initio protein structure predictions. Journal of Structural Biology. 134: 186-90. PMID 11551178 DOI: 10.1006/Jsbi.2000.4370 |
0.341 |
|
| 2001 |
Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. Conversion of monomeric protein L to an obligate dimer by computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 98: 10687-91. PMID 11526208 DOI: 10.1073/Pnas.181354398 |
0.32 |
|
| 2001 |
Nauli S, Kuhlman B, Baker D. Computer-based redesign of a protein folding pathway. Nature Structural Biology. 8: 602-5. PMID 11427890 DOI: 10.1038/89638 |
0.335 |
|
| 2001 |
Bonneau R, Baker D. Ab initio protein structure prediction: progress and prospects. Annual Review of Biophysics and Biomolecular Structure. 30: 173-89. PMID 11340057 DOI: 10.1146/Annurev.Biophys.30.1.173 |
0.319 |
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| 2001 |
Minard P, Scalley-Kim M, Watters A, Baker D. A "loop entropy reduction" phage-display selection for folded amino acid sequences. Protein Science : a Publication of the Protein Society. 10: 129-34. PMID 11266601 DOI: 10.1110/Ps.32401 |
0.334 |
|
| 2001 |
O'Neill JW, Kim DE, Baker D, Zhang KY. Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution. Acta Crystallographica. Section D, Biological Crystallography. 57: 480-7. PMID 11264576 DOI: 10.1107/S0907444901000373 |
0.333 |
|
| 2001 |
Simons KT, Strauss C, Baker D. Prospects for ab initio protein structural genomics. Journal of Molecular Biology. 306: 1191-9. PMID 11237627 DOI: 10.1006/Jmbi.2000.4459 |
0.368 |
|
| 2001 |
Hankey DJ, Lightman SL, Baker D. Interphotoreceptor retinoid binding protein peptide-induced uveitis in B10.RIII mice: characterization of disease parameters and immunomodulation. Experimental Eye Research. 72: 341-50. PMID 11180983 DOI: 10.1006/Exer.2000.0957 |
0.302 |
|
| 2001 |
Grantcharova V, Alm EJ, Baker D, Horwich AL. Mechanisms of protein folding. Current Opinion in Structural Biology. 11: 70-82. PMID 11179895 DOI: 10.1016/S0959-440X(00)00176-7 |
0.349 |
|
| 2001 |
Grantcharova VP, Baker D. Circularization changes the folding transition state of the src SH3 domain. Journal of Molecular Biology. 306: 555-63. PMID 11178913 DOI: 10.1006/Jmbi.2000.4352 |
0.317 |
|
| 2001 |
Bonneau R, Strauss CE, Baker D. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins. 43: 1-11. PMID 11170209 DOI: 10.1002/1097-0134(20010401)43:1<1::Aid-Prot1012>3.0.Co;2-A |
0.325 |
|
| 2000 |
Bowers PM, Strauss CE, Baker D. De novo protein structure determination using sparse NMR data. Journal of Biomolecular Nmr. 18: 311-8. PMID 11200525 DOI: 10.1023/A:1026744431105 |
0.358 |
|
| 2000 |
Plaxco KW, Simons KT, Ruczinski I, Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39: 11177-83. PMID 10985762 DOI: 10.1021/Bi000200N |
0.37 |
|
| 2000 |
Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proceedings of the National Academy of Sciences of the United States of America. 97: 10383-8. PMID 10984534 DOI: 10.1073/Pnas.97.19.10383 |
0.336 |
|
| 2000 |
McCallister EL, Alm E, Baker D. Critical role of β-hairpin formation in protein G folding Nature Structural Biology. 7: 669-673. PMID 10932252 DOI: 10.1038/77971 |
0.331 |
|
| 2000 |
Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. Journal of Molecular Biology. 301: 173-90. PMID 10926500 DOI: 10.1006/Jmbi.2000.3837 |
0.347 |
|
| 2000 |
Grantcharova VP, Riddle DS, Baker D. Long-range order in the src SH3 folding transition state. Proceedings of the National Academy of Sciences of the United States of America. 97: 7084-9. PMID 10860975 DOI: 10.1073/Pnas.97.13.7084 |
0.307 |
|
| 2000 |
Baker D. A surprising simplicity to protein folding. Nature. 405: 39-42. PMID 10811210 DOI: 10.1038/35011000 |
0.357 |
|
| 2000 |
Kim DE, Fisher C, Baker D. A breakdown of symmetry in the folding transition state of protein L. Journal of Molecular Biology. 298: 971-84. PMID 10801362 DOI: 10.1006/Jmbi.2000.3701 |
0.304 |
|
| 2000 |
Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D. Evolutionary conservation in protein folding kinetics. Journal of Molecular Biology. 298: 303-12. PMID 10764599 DOI: 10.1006/Jmbi.1999.3663 |
0.337 |
|
| 2000 |
Thoua NM, van Noort JM, Baker D, Bose A, van Sechel AC, van Stipdonk MJ, Travers PJ, Amor S. Encephalitogenic and immunogenic potential of the stress protein alphaB-crystallin in Biozzi ABH (H-2A(g7)) mice. Journal of Neuroimmunology. 104: 47-57. PMID 10683514 DOI: 10.1016/S0165-5728(99)00246-5 |
0.309 |
|
| 1999 |
Gu H, Doshi N, Kim DE, Simons KT, Santiago JV, Nauli S, Baker D. Robustness of protein folding kinetics to surface hydrophobic substitutions. Protein Science : a Publication of the Protein Society. 8: 2734-41. PMID 10631990 DOI: 10.1110/Ps.8.12.2734 |
0.31 |
|
| 1999 |
Scalley ML, Nauli S, Gladwin ST, Baker D. Structural transitions in the protein L denatured state ensemble. Biochemistry. 38: 15927-35. PMID 10625459 DOI: 10.1021/Bi991136G |
0.318 |
|
| 1999 |
Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nature Structural Biology. 6: 1016-24. PMID 10542092 DOI: 10.1038/14901 |
0.311 |
|
| 1999 |
Alm E, Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proceedings of the National Academy of Sciences of the United States of America. 96: 11305-10. PMID 10500172 DOI: 10.1073/Pnas.96.20.11305 |
0.341 |
|
| 1999 |
Plaxco KW, Millett IS, Segel DJ, Doniach S, Baker D. Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nature Structural Biology. 6: 554-6. PMID 10360359 DOI: 10.1038/9329 |
0.303 |
|
| 1999 |
Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 34: 82-95. PMID 10336385 DOI: 10.1002/(Sici)1097-0134(19990101)34:1<82::Aid-Prot7>3.0.Co;2-A |
0.353 |
|
| 1999 |
Alm E, Baker D. Matching theory and experiment in protein folding. Current Opinion in Structural Biology. 9: 189-96. PMID 10322214 DOI: 10.1016/S0959-440X(99)80027-X |
0.349 |
|
| 1999 |
Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA Proteins: Structure, Function, and Genetics. 37: 171-176. DOI: 10.1002/(Sici)1097-0134(1999)37:3+<171::Aid-Prot21>3.0.Co;2-Z |
0.346 |
|
| 1998 |
Kim DE, Yi Q, Gladwin ST, Goldberg JM, Baker D. The single helix in protein L is largely disrupted at the rate-limiting step in folding. Journal of Molecular Biology. 284: 807-15. PMID 9826517 DOI: 10.1006/Jmbi.1998.2200 |
0.327 |
|
| 1998 |
Plaxco KW, Baker D. Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proceedings of the National Academy of Sciences of the United States of America. 95: 13591-6. PMID 9811844 DOI: 10.1073/Pnas.95.23.13591 |
0.311 |
|
| 1998 |
Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. Journal of Molecular Biology. 283: 293-300. PMID 9761691 DOI: 10.1006/Jmbi.1998.2072 |
0.317 |
|
| 1998 |
Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proceedings of the National Academy of Sciences of the United States of America. 95: 11158-62. PMID 9736706 DOI: 10.1073/Pnas.95.19.11158 |
0.341 |
|
| 1998 |
Grantcharova VP, Riddle DS, Santiago JV, Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nature Structural Biology. 5: 714-20. PMID 9699636 DOI: 10.1038/1412 |
0.31 |
|
| 1998 |
Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of Molecular Biology. 281: 565-77. PMID 9698570 DOI: 10.1006/Jmbi.1998.1943 |
0.348 |
|
| 1998 |
Kim DE, Gu H, Baker D. The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proceedings of the National Academy of Sciences of the United States of America. 95: 4982-6. PMID 9560214 DOI: 10.1073/Pnas.95.9.4982 |
0.345 |
|
| 1998 |
Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. Journal of Molecular Biology. 277: 985-94. PMID 9545386 DOI: 10.1006/Jmbi.1998.1645 |
0.325 |
|
| 1998 |
Plaxco KW, Riddle DS, Grantcharova V, Baker D. Simplified proteins: minimalist solutions to the 'protein folding problem'. Current Opinion in Structural Biology. 8: 80-5. PMID 9519299 DOI: 10.1016/S0959-440X(98)80013-4 |
0.354 |
|
| 1998 |
Gu H, Kim D, Baker D. Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. Journal of Molecular Biology. 274: 588-96. PMID 9417937 DOI: 10.1006/Jmbi.1997.1374 |
0.31 |
|
| 1997 |
Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins. 167-71. PMID 9485508 DOI: 10.1002/(Sici)1097-0134(1997)1+<167::Aid-Prot21>3.0.Co;2-L |
0.3 |
|
| 1997 |
Grantcharova VP, Baker D. Folding dynamics of the src SH3 domain. Biochemistry. 36: 15685-92. PMID 9398297 DOI: 10.1021/Bi971786P |
0.307 |
|
| 1997 |
Yi Q, Scalley ML, Simons KT, Gladwin ST, Baker D. Characterization of the free energy spectrum of peptostreptococcal protein L. Folding & Design. 2: 271-80. PMID 9377710 DOI: 10.1016/S1359-0278(97)00038-2 |
0.302 |
|
| 1997 |
Doyle R, Simons K, Qian H, Baker D. Local interactions and the optimization of protein folding. Proteins. 29: 282-91. PMID 9365984 DOI: 10.1002/(Sici)1097-0134(199711)29:3<282::Aid-Prot3>3.0.Co;2-D |
0.312 |
|
| 1997 |
Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D. Functional rapidly folding proteins from simplified amino acid sequences. Nature Structural Biology. 4: 805-9. PMID 9334745 DOI: 10.1038/Nsb1097-805 |
0.337 |
|
| 1997 |
Han KF, Bystroff C, Baker D. Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Science : a Publication of the Protein Society. 6: 1587-90. PMID 9232660 DOI: 10.1002/Pro.5560060723 |
0.31 |
|
| 1997 |
Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. Journal of Molecular Biology. 268: 209-25. PMID 9149153 DOI: 10.1006/Jmbi.1997.0959 |
0.362 |
|
| 1997 |
Scalley ML, Yi Q, Gu H, McCormack A, Yates JR, Baker D. Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. Biochemistry. 36: 3373-82. PMID 9116017 DOI: 10.1021/Bi9625758 |
0.307 |
|
| 1996 |
Bystroff C, Simons KT, Han KF, Baker D. Local sequence-structure correlations in proteins. Current Opinion in Biotechnology. 7: 417-21. PMID 8768900 DOI: 10.1016/S0958-1669(96)80117-0 |
0.33 |
|
| 1996 |
Han KF, Baker D. Global properties of the mapping between local amino acid sequence and local structure in proteins. Proceedings of the National Academy of Sciences of the United States of America. 93: 5814-8. PMID 8650175 DOI: 10.1073/Pnas.93.12.5814 |
0.323 |
|
| 1995 |
Gu H, Yi Q, Bray ST, Riddle DS, Shiau AK, Baker D. A phage display system for studying the sequence determinants of protein folding. Protein Science : a Publication of the Protein Society. 4: 1108-17. PMID 7549875 DOI: 10.1002/Pro.5560040609 |
0.332 |
|
| 1994 |
Baker D, Agard DA. Kinetics versus thermodynamics in protein folding. Biochemistry. 33: 7505-9. PMID 8011615 DOI: 10.1021/Bi00190A002 |
0.339 |
|
| 1993 |
Bystroff C, Baker D, Fletterick RJ, Agard DA. PRISM: application to the solution of two protein structures. Acta Crystallographica. Section D, Biological Crystallography. 49: 440-8. PMID 15299503 DOI: 10.1107/S0907444993004020 |
0.311 |
|
| 1992 |
Baker D, Silen JL, Agard DA. Protease pro region required for folding is a potent inhibitor of the mature enzyme. Proteins. 12: 339-44. PMID 1579568 DOI: 10.1002/Prot.340120406 |
0.304 |
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