| Year |
Citation |
Score |
| 2023 |
Muenks A, Zepeda S, Zhou G, Veesler D, DiMaio F. Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps. Nature Communications. 14: 1164. PMID 36859493 DOI: 10.1038/s41467-023-36732-5 |
0.313 |
|
| 2022 |
Lugmayr W, Kotov V, Goessweiner-Mohr N, Wald J, DiMaio F, Marlovits TC. StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement. Nature Protocols. PMID 36323866 DOI: 10.1038/s41596-022-00757-9 |
0.325 |
|
| 2022 |
Cummins MC, Jacobs TM, Teets FD, DiMaio F, Tripathy A, Kuhlman B. AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein. Protein Science : a Publication of the Protein Society. 31: e4368. PMID 35762713 DOI: 10.1002/pro.4368 |
0.319 |
|
| 2020 |
Pavlovicz RE, Park H, DiMaio F. Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination. Plos Computational Biology. 16: e1008103. PMID 32956350 DOI: 10.1371/Journal.Pcbi.1008103 |
0.371 |
|
| 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 |
0.46 |
|
| 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, ... ... DiMaio F, et al. Computational design of transmembrane pores. Nature. PMID 32848250 DOI: 10.1038/S41586-020-2646-5 |
0.384 |
|
| 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 |
0.401 |
|
| 2020 |
Bhargava HK, Tabata K, Byck JM, Hamasaki M, Farrell DP, Anishchenko I, DiMaio F, Im YJ, Yoshimori T, Hurley JH. Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex. Proceedings of the National Academy of Sciences of the United States of America. PMID 32632011 DOI: 10.1073/Pnas.2008030117 |
0.351 |
|
| 2020 |
Al-Otaibi NS, Taylor AJ, Farrell DP, Tzokov SB, DiMaio F, Kelly DJ, Bergeron JRC. The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation. Nature Communications. 11: 3210. PMID 32587243 DOI: 10.1038/S41467-020-16981-4 |
0.392 |
|
| 2020 |
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... DiMaio F, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2 |
0.307 |
|
| 2020 |
Evans EGB, Morgan JLW, DiMaio F, Zagotta WN, Stoll S. Allosteric conformational change of a cyclic nucleotide-gated ion channel revealed by DEER spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. PMID 32358188 DOI: 10.1073/Pnas.1916375117 |
0.309 |
|
| 2019 |
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, et al. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure (London, England : 1993). PMID 31780431 DOI: 10.1016/J.Str.2019.11.002 |
0.401 |
|
| 2019 |
Chou HT, Apelt L, Farrell DP, White SR, Woodsmith J, Svetlov V, Goldstein JS, Nager AR, Li Z, Muller J, Dollfus H, Nudler E, Stelzl U, DiMaio F, Nachury MV, et al. The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach. Structure (London, England : 1993). PMID 31303482 DOI: 10.1016/J.Str.2019.06.006 |
0.436 |
|
| 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, ... ... DiMaio F, et al. De novo protein design by citizen scientists. Nature. PMID 31168091 DOI: 10.1038/S41586-019-1274-4 |
0.408 |
|
| 2019 |
Rizo AN, Lin J, Gates SN, Tse E, Bart SM, Castellano LM, DiMaio F, Shorter J, Southworth DR. Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase. Nature Communications. 10: 2393. PMID 31160557 DOI: 10.1038/S41467-019-10150-Y |
0.377 |
|
| 2019 |
Wang F, Cvirkaite-Krupovic V, Kreutzberger MAB, Su Z, de Oliveira GAP, Osinski T, Sherman N, DiMaio F, Wall JS, Prangishvili D, Krupovic M, Egelman EH. An extensively glycosylated archaeal pilus survives extreme conditions. Nature Microbiology. PMID 31110358 DOI: 10.1038/S41564-019-0458-X |
0.409 |
|
| 2019 |
Chen Z, Johnson MC, Chen J, Bick MJ, Boyken SE, Lin B, De Yoreo JJ, Kollman JM, Baker D, DiMaio F. Self-assembling 2D arrays with de novo protein building blocks. Journal of the American Chemical Society. PMID 31050411 DOI: 10.1021/Jacs.9B01978 |
0.317 |
|
| 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, et al. Programmable design of orthogonal protein heterodimers. Nature. 565: 106-111. PMID 30568301 DOI: 10.1038/s41586-018-0802-y |
0.35 |
|
| 2019 |
Lahiri I, Xu J, Han BG, Oh J, Wang D, DiMaio F, Leschziner AE. 3.1 angstrom structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids. Journal of Structural Biology. 207: 270-278. DOI: 10.2210/Pdb6O6C/Pdb |
0.368 |
|
| 2019 |
Walls AC, Tortorici MA, Xiong X, Snijder J, Frenz B, Bosch B, DiMaio F, Corti D, Rey FA, Veesler D. Structural Studies of Coronavirus Fusion Proteins Microscopy and Microanalysis. 25: 1300-1301. DOI: 10.1017/S1431927619007232 |
0.402 |
|
| 2019 |
Reggiano G, DiMaio F. Processing Structurally Heterogeneous Cryo-EM Data Using Atomic Models Microscopy and Microanalysis. 25: 228-229. DOI: 10.1017/S1431927619001879 |
0.362 |
|
| 2019 |
Chen Z, Suzuki H, Kobayashi Y, Wang AC, DiMaio F, Kawashima SA, Walz T, Kapoor TM. Structural Insights into Mdn1, an ∼540 kDa AAA Protein Required for Ribosome Biogenesis Biophysical Journal. 116: 17a. DOI: 10.1016/J.Bpj.2018.11.133 |
0.411 |
|
| 2018 |
Park YJ, Lacourse KD, Cambillau C, DiMaio F, Mougous JD, Veesler D. Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy. Nature Communications. 9: 5385. PMID 30568167 DOI: 10.2210/Pdb6N38/Pdb |
0.411 |
|
| 2018 |
Frenz B, Rämisch S, Borst AJ, Walls AC, Adolf-Bryfogle J, Schief WR, Veesler D, DiMaio F. Automatically Fixing Errors in Glycoprotein Structures with Rosetta. Structure (London, England : 1993). PMID 30344107 DOI: 10.1016/J.Str.2018.09.006 |
0.412 |
|
| 2018 |
Sui X, Arlt H, Brock KP, Lai ZW, DiMaio F, Marks DS, Liao M, Farese RV, Walther TC. Cryo-electron microscopy structure of the lipid droplet-formation protein seipin. The Journal of Cell Biology. PMID 30327422 DOI: 10.1083/Jcb.201809067 |
0.398 |
|
| 2018 |
Chen Z, Suzuki H, Kobayashi Y, Wang AC, DiMaio F, Kawashima SA, Walz T, Kapoor TM. Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis. Cell. PMID 30318141 DOI: 10.1016/J.Cell.2018.09.015 |
0.398 |
|
| 2018 |
Kellogg EH, Hejab NMA, Poepsel S, Downing KH, DiMaio F, Nogales E. Near-atomic model of microtubule-tau interactions. Science (New York, N.Y.). PMID 29748322 DOI: 10.1126/Science.Aat1780 |
0.317 |
|
| 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 |
0.366 |
|
| 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 |
0.36 |
|
| 2018 |
Usluer GD, DiMaio F, Yang SK, Hansen JM, Polka JK, Mullins RD, Kollman JM. Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain. Proceedings of the National Academy of Sciences of the United States of America. PMID 29440491 DOI: 10.1073/Pnas.1715836115 |
0.372 |
|
| 2017 |
Martin GM, Kandasamy B, DiMaio F, Yoshioka C, Shyng SL. Anti-diabetic drug binding site in a mammalian KATP channels revealed by Cryo-EM. Elife. 6. PMID 29035201 DOI: 10.7554/Elife.31054 |
0.321 |
|
| 2017 |
Borst AJ, James ZM, Zagotta WN, Ginsberg M, Rey FA, DiMaio F, Backovic M, Veesler D. The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human αVβ3 Integrin via Steric Hindrance. Structure (London, England : 1993). PMID 29033288 DOI: 10.1016/J.Str.2017.09.007 |
0.31 |
|
| 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 |
0.445 |
|
| 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 |
0.394 |
|
| 2017 |
Ve T, Vajjhala PR, Hedger A, Croll T, DiMaio F, Horsefield S, Yu X, Lavrencic P, Hassan Z, Morgan GP, Mansell A, Mobli M, O'Carroll A, Chauvin B, Gambin Y, et al. Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling. Nature Structural & Molecular Biology. PMID 28759049 DOI: 10.1038/Nsmb.3444 |
0.326 |
|
| 2017 |
Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature. PMID 28682307 DOI: 10.1038/Nature23314 |
0.338 |
|
| 2017 |
Frenz B, Walls AC, Egelman EH, Veesler D, DiMaio F. RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Nature Methods. PMID 28628127 DOI: 10.1038/Nmeth.4340 |
0.423 |
|
| 2017 |
DiMaio F. Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems. Methods of Molecular Biology. 1607: 455-466. PMID 28573585 DOI: 10.1007/978-1-4939-7000-1_19 |
0.411 |
|
| 2017 |
James ZM, Borst AJ, Haitin Y, Frenz B, DiMaio F, Zagotta WN, Veesler D. CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Proceedings of the National Academy of Sciences of the United States of America. PMID 28396445 DOI: 10.1073/Pnas.1700248114 |
0.32 |
|
| 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 |
0.392 |
|
| 2016 |
Fu TM, Li Y, Lu A, Li Z, Vajjhala PR, Cruz AC, Srivastava DB, DiMaio F, Penczek PA, Siegel RM, Stacey KJ, Egelman EH, Wu H. Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex. Molecular Cell. PMID 27746017 DOI: 10.1016/J.Molcel.2016.09.009 |
0.339 |
|
| 2016 |
Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. Elife. 5. PMID 27669148 DOI: 10.7554/Elife.17219 |
0.414 |
|
| 2016 |
Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ. Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35. Proteins. PMID 27667482 DOI: 10.1002/Prot.25168 |
0.399 |
|
| 2016 |
Walls A, Tortorici MA, Bosch BJ, Frenz B, Rottier PJ, DiMaio F, Rey F, Veesler D. Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy. Protein Science : a Publication of the Protein Society. PMID 27667334 DOI: 10.1002/Pro.3048 |
0.374 |
|
| 2016 |
Walls AC, Tortorici MA, Frenz B, Snijder J, Li W, Rey FA, DiMaio F, Bosch BJ, Veesler D. Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Nature Structural & Molecular Biology. PMID 27617430 DOI: 10.1038/Nsmb.3293 |
0.37 |
|
| 2016 |
DiMaio F, Chiu W. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps. Methods in Enzymology. 579: 255-76. PMID 27572730 DOI: 10.1016/Bs.Mie.2016.06.003 |
0.383 |
|
| 2016 |
Bender BJ, Cisneros A, Duran AM, Finn JA, Fu D, Lokits AD, Mueller BK, Sangha AK, Sauer MF, Sevy AM, Sliwoski G, Sheehan JH, DiMaio F, Meiler J, Moretti R. Protocols for Molecular Modeling with Rosetta3 and RosettaScripts. Biochemistry. PMID 27490953 DOI: 10.1021/Acs.Biochem.6B00444 |
0.391 |
|
| 2016 |
Conway P, DiMaio F. Improving hybrid statistical and physical forcefields through local structure enumeration. Protein Science : a Publication of the Protein Society. PMID 27239808 DOI: 10.1002/Pro.2956 |
0.347 |
|
| 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 |
0.329 |
|
| 2016 |
Walls AC, Tortorici MA, Bosch BJ, Frenz B, Rottier PJ, DiMaio F, Rey FA, Veesler D. Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature. 531: 114-7. PMID 26855426 DOI: 10.1038/Nature16988 |
0.412 |
|
| 2016 |
Hospenthal MK, Redzej A, Dodson K, Ukleja M, Frenz B, Rodrigues C, Hultgren SJ, DiMaio F, Egelman EH, Waksman G. Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling. Cell. 164: 269-78. PMID 26724865 DOI: 10.1016/J.Cell.2015.11.049 |
0.379 |
|
| 2016 |
Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. Author response: Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta Elife. DOI: 10.7554/Elife.17219.029 |
0.35 |
|
| 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 |
0.406 |
|
| 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 |
0.33 |
|
| 2015 |
Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nature Methods. 12: 943-6. PMID 26280328 DOI: 10.1038/Nmeth.3541 |
0.339 |
|
| 2015 |
Park H, DiMaio F, Baker D. CASP11 refinement experiments with ROSETTA. Proteins. PMID 26205421 DOI: 10.1002/Prot.24862 |
0.428 |
|
| 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 |
0.392 |
|
| 2015 |
DiMaio F, Chen CC, Yu X, Frenz B, Hsu YH, Lin NS, Egelman EH. The molecular basis for flexibility in the flexible filamentous plant viruses. Nature Structural & Molecular Biology. PMID 26167882 DOI: 10.1038/Nsmb.3054 |
0.352 |
|
| 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 |
0.358 |
|
| 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 |
0.325 |
|
| 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 |
0.422 |
|
| 2015 |
O'Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. Journal of Chemical Theory and Computation. 11: 609-622. PMID 25866491 DOI: 10.1021/Ct500864R |
0.329 |
|
| 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 |
0.414 |
|
| 2015 |
DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits TC, Cheng Y, Baker D. Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nature Methods. 12: 361-5. PMID 25707030 DOI: 10.1038/Nmeth.3286 |
0.355 |
|
| 2015 |
Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nature Methods. 12: 335-8. PMID 25707029 DOI: 10.1038/Nmeth.3287 |
0.407 |
|
| 2015 |
Solomonson M, Setiaputra D, Makepeace KA, Lameignere E, Petrotchenko EV, Conrady DG, Bergeron JR, Vuckovic M, DiMaio F, Borchers CH, Yip CK, Strynadka NC. Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism. Structure (London, England : 1993). 23: 571-83. PMID 25684576 DOI: 10.1016/J.Str.2015.01.002 |
0.41 |
|
| 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 |
0.408 |
|
| 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 |
0.364 |
|
| 2014 |
Gawarzewski I, DiMaio F, Winterer E, Tschapek B, Smits SH, Jose J, Schmitt L. Crystal structure of the transport unit of the autotransporter adhesin involved in diffuse adherence from Escherichia coli. Journal of Structural Biology. 187: 20-9. PMID 24841284 DOI: 10.1016/J.Jsb.2014.05.003 |
0.317 |
|
| 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 |
0.409 |
|
| 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 |
0.441 |
|
| 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 |
0.473 |
|
| 2013 |
DiMaio F. Advances in Rosetta structure prediction for difficult molecular-replacement problems. Acta Crystallographica. Section D, Biological Crystallography. 69: 2202-8. PMID 24189231 DOI: 10.1107/S0907444913023305 |
0.384 |
|
| 2013 |
DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods. 10: 1102-4. PMID 24076763 DOI: 10.1107/S2053273314092171 |
0.354 |
|
| 2013 |
Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D. High-resolution comparative modeling with RosettaCM. Structure (London, England : 1993). 21: 1735-42. PMID 24035711 DOI: 10.1016/J.Str.2013.08.005 |
0.365 |
|
| 2013 |
Brelidze TI, Gianulis EC, DiMaio F, Trudeau MC, Zagotta WN. Structure of the C-terminal region of an ERG channel and functional implications. Proceedings of the National Academy of Sciences of the United States of America. 110: 11648-53. PMID 23801759 DOI: 10.1073/Pnas.1306887110 |
0.306 |
|
| 2013 |
Bergeron JR, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NC. A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. Plos Pathogens. 9: e1003307. PMID 23633951 DOI: 10.1371/Journal.Ppat.1003307 |
0.383 |
|
| 2013 |
DiMaio F, Zhang J, Chiu W, Baker D. Cryo-EM model validation using independent map reconstructions. Protein Science : a Publication of the Protein Society. 22: 865-8. PMID 23592445 DOI: 10.1002/Pro.2267 |
0.362 |
|
| 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 |
0.394 |
|
| 2013 |
Brelidze TI, DiMaio F, Trudeau MC, Zagotta WN. Structure of the C-Terminal Region of an ERG Channel and Functional Implications for Long-QT Syndrome Biophysical Journal. 104: 356a. DOI: 10.1016/J.Bpj.2012.11.1978 |
0.303 |
|
| 2013 |
Dimaio F. Protein structure modeling with Rosetta: Case studies in structure prediction and enzyme repurposing Nato Science For Peace and Security Series a: Chemistry and Biology. 353-362. DOI: 10.1007/978-94-007-6232-9-31 |
0.328 |
|
| 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 |
0.373 |
|
| 2012 |
Bankston JR, Camp SS, DiMaio F, Lewis AS, Chetkovich DM, Zagotta WN. Structure and stoichiometry of an accessory subunit TRIP8b interaction with hyperpolarization-activated cyclic nucleotide-gated channels. Proceedings of the National Academy of Sciences of the United States of America. 109: 7899-904. PMID 22550182 DOI: 10.1073/Pnas.1201997109 |
0.335 |
|
| 2012 |
Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. Journal of Structural and Functional Genomics. 13: 81-90. PMID 22418934 DOI: 10.1007/S10969-012-9129-3 |
0.38 |
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| 2012 |
Terwilliger TC, DiMaio F, Read RJ, Baker D, Brunger AT, Adams PD. Molecular replacement and model-building using distant homology models as templates Acta Crystallographica Section a Foundations of Crystallography. 68: s17-s18. DOI: 10.1107/S0108767312099667 |
0.331 |
|
| 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 |
0.439 |
|
| 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 |
0.439 |
|
| 2011 |
Valkov E, Stamp A, Dimaio F, Baker D, Verstak B, Roversi P, Kellie S, Sweet MJ, Mansell A, Gay NJ, Martin JL, Kobe B. Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection. Proceedings of the National Academy of Sciences of the United States of America. 108: 14879-84. PMID 21873236 DOI: 10.1073/Pnas.1104780108 |
0.363 |
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| 2011 |
DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I. Modeling symmetric macromolecular structures in Rosetta3. Plos One. 6: e20450. PMID 21731614 DOI: 10.1371/Journal.Pone.0020450 |
0.44 |
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| 2011 |
Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak LA, Baker D, Frydman J, Levitt M, Chiu W. Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. Structure (London, England : 1993). 19: 633-9. PMID 21565698 DOI: 10.1016/J.Str.2011.03.005 |
0.356 |
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| 2011 |
Lyskowski A, Oeemig JS, Jaakkonen A, Rommi K, DiMaio F, Zhou D, Kajander T, Baker D, Wlodawer A, Goldman A, Iwaï H. Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 67: 623-6. PMID 21543876 DOI: 10.1107/S1744309111008372 |
0.321 |
|
| 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 |
0.468 |
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| 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 |
0.439 |
|
| 2011 |
Li M, Dimaio F, Zhou D, Gustchina A, Lubkowski J, Dauter Z, Baker D, Wlodawer A. Crystal structure of XMRV protease differs from the structures of other retropepsins. Nature Structural & Molecular Biology. 18: 227-9. PMID 21258323 DOI: 10.1038/Nsmb.1964 |
0.374 |
|
| 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 |
0.437 |
|
| 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 |
0.449 |
|
| 2011 |
Read RJ, McCoy AJ, Terwilliger TC, DiMaio F, Baker D. Extending the limits in solving and rebuilding molecular replacement structures Acta Crystallographica Section A. 67: 64-64. DOI: 10.1107/S010876731109845X |
0.37 |
|
| 2010 |
Baker ML, Baker MR, Hryc CF, Dimaio F. Analyses of subnanometer resolution cryo-EM density maps. Methods in Enzymology. 483: 1-29. PMID 20888467 DOI: 10.1016/S0076-6879(10)83001-0 |
0.393 |
|
| 2010 |
Yarov-Yarovoy VM, DiMaio F, Scheuer T, Baker D, Catterall WA. High-Resolution Structural Modeling of Ion Channel Pore-Forming Domains Using Rosetta Biophysical Journal. 98: 117a. DOI: 10.1016/J.Bpj.2009.12.640 |
0.363 |
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| 2009 |
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77: 89-99. PMID 19701941 DOI: 10.1002/Prot.22540 |
0.426 |
|
| 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 |
0.393 |
|
| 2007 |
DiMaio F, Kondrashov DA, Bitto E, Soni A, Bingman CA, Phillips GN, Shavlik JW. Creating protein models from electron-density maps using particle-filtering methods. Bioinformatics (Oxford, England). 23: 2851-8. PMID 17933855 DOI: 10.1093/Bioinformatics/Btm480 |
0.353 |
|
| 2006 |
DiMaio F, Shavlik J, Phillips GN. A probabilistic approach to protein backbone tracing in electron density maps. Bioinformatics (Oxford, England). 22: e81-9. PMID 16873525 DOI: 10.1093/Bioinformatics/Btl252 |
0.383 |
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