| Accurate prediction of protein structures and interactions using a three-track neural network M Baek, F DiMaio, I Anishchenko, J Dauparas, S Ovchinnikov, GR Lee, ... Science 373 (6557), 871-876, 2021 | 5911 | 2021 |
| De novo design of protein structure and function with RFdiffusion JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim, HE Eisenach, ... Nature 620 (7976), 1089-1100, 2023 | 2175 | 2023 |
| The Rosetta all-atom energy function for macromolecular modeling and design RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ... Journal of chemical theory and computation 13 (6), 3031-3048, 2017 | 1809 | 2017 |
| High-resolution comparative modeling with RosettaCM Y Song, F DiMaio, RYR Wang, D Kim, C Miles, TJ Brunette, J Thompson, ... Structure 21 (10), 1735-1742, 2013 | 1308 | 2013 |
| Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020 | 934 | 2020 |
| Generalized biomolecular modeling and design with RoseTTAFold All-Atom R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh, I Kalvet, GR Lee, ... Science 384 (6693), eadl2528, 2024 | 927 | 2024 |
| EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy BA Barad, N Echols, RYR Wang, Y Cheng, F DiMaio, PD Adams, ... Nature methods 12 (10), 943-946, 2015 | 910 | 2015 |
| Crystal structure of a monomeric retroviral protease solved by protein folding game players F Khatib, F DiMaio, Foldit Contenders Group, Foldit Void Crushers Group, ... Nature structural & molecular biology 18 (10), 1175-1177, 2011 | 703 | 2011 |
| De novo protein design by deep network hallucination I Anishchenko, SJ Pellock, TM Chidyausiku, TA Ramelot, S Ovchinnikov, ... Nature 600 (7889), 547-552, 2021 | 694 | 2021 |
| Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer AC Walls, MA Tortorici, BJ Bosch, B Frenz, PJM Rottier, F DiMaio, FA Rey, ... Nature 531 (7592), 114-117, 2016 | 633 | 2016 |
| Structure prediction for CASP8 with all‐atom refinement using Rosetta S Raman, R Vernon, J Thompson, M Tyka, R Sadreyev, J Pei, D Kim, ... Proteins: Structure, Function, and Bioinformatics 77 (S9), 89-99, 2009 | 628 | 2009 |
| Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules H Park, P Bradley, P Greisen Jr, Y Liu, VK Mulligan, DE Kim, D Baker, ... Journal of chemical theory and computation 12 (12), 6201-6212, 2016 | 610 | 2016 |
| Scaffolding protein functional sites using deep learning J Wang, S Lisanza, D Juergens, D Tischer, JL Watson, KM Castro, ... Science 377 (6604), 387-394, 2022 | 498 | 2022 |
| Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta RYR Wang, Y Song, BA Barad, Y Cheng, JS Fraser, F DiMaio elife 5, e17219, 2016 | 495 | 2016 |
| Relaxation of backbone bond geometry improves protein energy landscape modeling P Conway, MD Tyka, F DiMaio, DE Konerding, D Baker Protein science 23 (1), 47-55, 2014 | 477 | 2014 |
| Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy AC Walls, MA Tortorici, B Frenz, J Snijder, W Li, FA Rey, F DiMaio, ... Nature structural & molecular biology 23 (10), 899-905, 2016 | 460 | 2016 |
| Near-atomic model of microtubule-tau interactions EH Kellogg, NMA Hejab, S Poepsel, KH Downing, F DiMaio, E Nogales Science 360 (6394), 1242-1246, 2018 | 458 | 2018 |
| Alternate states of proteins revealed by detailed energy landscape mapping MD Tyka, DA Keedy, I André, F DiMaio, Y Song, DC Richardson, ... Journal of molecular biology 405 (2), 607-618, 2011 | 453 | 2011 |
| De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity SE Boyken, Z Chen, B Groves, RA Langan, G Oberdorfer, A Ford, ... Science 352 (6286), 680-687, 2016 | 410 | 2016 |
| Improving de novo protein binder design with deep learning NR Bennett, B Coventry, I Goreshnik, B Huang, A Allen, D Vafeados, ... Nature Communications 14 (1), 2625, 2023 | 404 | 2023 |
