| 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 | 1131 | 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 | 562 | 2020 |
| Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing TA Whitehead, A Chevalier, Y Song, C Dreyfus, SJ Fleishman, ... Nature biotechnology 30 (6), 543-548, 2012 | 444 | 2012 |
| 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 | 394 | 2016 |
| Accurate de novo design of hyperstable constrained peptides G Bhardwaj, VK Mulligan, CD Bahl, JM Gilmore, PJ Harvey, O Cheneval, ... Nature 538 (7625), 329-335, 2016 | 384 | 2016 |
| 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 | 355 | 2011 |
| Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement F DiMaio, Y Song, X Li, MJ Brunner, C Xu, V Conticello, E Egelman, ... Nature methods 12 (4), 361-365, 2015 | 330 | 2015 |
| MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling Y Song, J Mao, MR Gunner Journal of computational chemistry 30 (14), 2231-2247, 2009 | 267 | 2009 |
| Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis SD Khare, Y Kipnis, PJ Greisen, R Takeuchi, Y Ashani, M Goldsmith, ... Nature chemical biology 8 (3), 294-300, 2012 | 255 | 2012 |
| Scientific benchmarks for guiding macromolecular energy function improvement A Leaver-Fay, MJ O'Meara, M Tyka, R Jacak, Y Song, EH Kellogg, ... Methods in enzymology 523, 109-143, 2013 | 244 | 2013 |
| Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples OF Lange, P Rossi, NG Sgourakis, Y Song, HW Lee, JM Aramini, ... Proceedings of the National Academy of Sciences 109 (27), 10873-10878, 2012 | 224 | 2012 |
| A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells E Procko, GY Berguig, BW Shen, Y Song, S Frayo, AJ Convertine, ... Cell 157 (7), 1644-1656, 2014 | 141 | 2014 |
| One contact for every twelve residues allows robust and accurate topology‐level protein structure modeling DE Kim, F DiMaio, R Yu‐Ruei Wang, Y Song, D Baker Proteins: Structure, Function, and Bioinformatics 82, 208-218, 2014 | 116 | 2014 |
| Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations MR Gunner, J Mao, Y Song, J Kim Biochimica et Biophysica Acta (BBA)-Bioenergetics 1757 (8), 942-968, 2006 | 112 | 2006 |
| Calculated Proton Uptake on Anaerobic Reduction of Cytochrome c Oxidase: Is the Reaction Electroneutral? Y Song, E Michonova-Alexova, MR Gunner Biochemistry 45 (26), 7959-7975, 2006 | 87 | 2006 |
| Calculation of proton transfers in bacteriorhodopsin bR and M intermediates Y Song, J Mao, MR Gunner Biochemistry 42 (33), 9875-9888, 2003 | 82 | 2003 |
| Prediction of protein mutational free energy: benchmark and sampling improvements increase classification accuracy B Frenz, SM Lewis, I King, F DiMaio, H Park, Y Song Frontiers in bioengineering and biotechnology 8, 558247, 2020 | 66 | 2020 |
| Structure‐guided forcefield optimization Y Song, M Tyka, A Leaver‐Fay, J Thompson, D Baker Proteins: Structure, Function, and Bioinformatics 79 (6), 1898-1909, 2011 | 66 | 2011 |
| Using multiconformation continuum electrostatics to compare chloride binding motifs in α-amylase, human serum albumin, and Omp32 Y Song, MR Gunner Journal of molecular biology 387 (4), 840-856, 2009 | 52 | 2009 |
| Trapping a transition state in a computationally designed protein bottle AD Pearson, JH Mills, Y Song, F Nasertorabi, GW Han, D Baker, ... Science 347 (6224), 863-867, 2015 | 42 | 2015 |
David BakerUniversity of WashingtonVerified email at uw.edu
