Yifan Song
Yifan Song
Cyrus Biotechnology
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Cited by
Cited by
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
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
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
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
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
Atomic-accuracy models from 4.5-Ĺ 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
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
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
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
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
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
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
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
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
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
Calculation of proton transfers in bacteriorhodopsin bR and M intermediates
Y Song, J Mao, MR Gunner
Biochemistry 42 (33), 9875-9888, 2003
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
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, 1175, 2020
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
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
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