Halorhodopsin pumps Cl(–) and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions

Por Song, Yifan, Gunner, M. R.
Publicado no Proc Natl Acad Sci U S A (2014)

MCCE2: Improving Protein pK(a) Calculations with Extensive Side Chain Rotamer Sampling

Por SONG, YIFAN, MAO, JUNJUN, GUNNER, M. R.
Publicado em 2009

Electrostatic Environment of Hemes in Proteins: pK(a)s of Hydroxyl Ligands

Por Song, Yifan, Mao, Junjun, Gunner, M. R.
Publicado em 2006

Calculated Proton Uptake on Anaerobic Reduction of Cytochrome c Oxidase: Is the Reaction Electroneutral?

Por Song, Yifan, Michonova-Alexova, Ekaterina, Gunner, M. R.
Publicado em 2006

Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations?

Por Gunner, M.R., Mao, Junjun, Song, Yifan, Kim, Jinrang
Publicado em 2006

Pseudorevertants of a Semliki Forest Virus Fusion-Blocking Mutation Reveal a Critical Interchain Interaction in the Core Trimer

Por Liu, Catherine Y., Besanceney, Christen, Song, Yifan, Kielian, Margaret
Publicado em 2010

Structure-guided forcefield optimization

Por Song, Yifan, Tyka, Michael, Leaver-Fay, Andrew, Thompson, James, Baker, David
Publicado em 2011

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

Por Kim, David E., DiMaio, Frank, Wang, Ray Yu-Ruei, Song, Yifan, Baker, David
Publicado em 2013

Massively parallel determination and modeling of endonuclease substrate specificity

Por Thyme, Summer B., Song, Yifan, Brunette, T. J., Szeto, Mindy D., Kusak, Lara, Bradley, Philip, Baker, David
Publicado no Nucleic Acids Res (2014)

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

Por Wang, Ray Yu-Ruei, Song, Yifan, Barad, Benjamin A, Cheng, Yifan, Fraser, James S, DiMaio, Frank
Publicado no eLife (2016)

Prevalence of diabetic retinopathy among 13473 patients with diabetes mellitus in China: a cross-sectional epidemiological survey in six provinces

Por Liu, Yan, Song, Yifan, Tao, Liyuan, Qiu, Weiqiang, Lv, Huibin, Jiang, Xiaodan, Zhang, Mingzhou, Li, Xuemin
Publicado no BMJ Open (2017)

High resolution comparative modeling with RosettaCM

Por Song, Yifan, DiMaio, Frank, Wang, Ray Yu-Ruei, Kim, David, Miles, Chris, Brunette, TJ, Thompson, James, Baker, David
Publicado em 2013

Alternate states of proteins revealed by detailed energy landscape mapping

Por Tyka, Michael D., Keedy, Daniel A., André, Ingemar, DiMaio, Frank, Song, Yifan, Richardson, David C., Richardsonb, Jane S., Baker, David
Publicado em 2010

Crystal Structure of a Kinetically Persistent Transition State in a Computationally Designed Protein Bottle

Por Pearson, Aaron D., Mills, Jeremy H., Song, Yifan, Nasertorabi, Fariborz, Han, Gye Won, Baker, David, Stevens, Raymond C., Schultz, Peter G.
Publicado no Science (2015)

Atomic accuracy models from 4.5 Å cryo-electron microscopy data with density-guided iterative local refinement

Por DiMaio, Frank, Song, Yifan, Li, Xueming, Brunner, Matthias J., Xu, Chunfu, Conticello, Vincent, Egelman, Edward, Marlovits, Thomas, Cheng, Yifan, Baker, David
Publicado no Nat Methods (2015)

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

Por Lange, Oliver F., Rossi, Paolo, Sgourakis, Nikolaos G., Song, Yifan, Lee, Hsiau-Wei, Aramini, James M., Ertekin, Asli, Xiao, Rong, Acton, Thomas B., Montelione, Gaetano T., Baker, David
Publicado em 2012

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

Por Whitehead, Timothy A, Chevalier, Aaron, Song, Yifan, Dreyfus, Cyrille, Fleishman, Sarel J, De Mattos, Cecilia, Myers, Chris A, Kamisetty, Hetunandan, Blair, Patrick, Wilson, Ian A, Baker, David
Publicado em 2012

Redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

Por Khare, Sagar D., Kipnis, Yakov, Greisen, Per, Takeuchi, Ryo, Ashani, Yacov, Goldsmith, Moshe, Song, Yifan, Gallaher, Jasmine L., Silman, Israel, Leader, Haim, Sussman, Joel L., Stoddard, Barry L., Tawfik, Dan S., Baker, David
Publicado em 2012

A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells

Por Procko, Erik, Berguig, Geoffrey Y., Shen, Betty W., Song, Yifan, Frayo, Shani, Convertine, Anthony J., Margineantu, Daciana, Booth, Garrett, Correia, Bruno E., Cheng, Yuanhua, Schief, William R., Hockenbery, David M., Press, Oliver W., Stoddard, Barry L., Stayton, Patrick S., Baker, David
Publicado em 2014

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement

Por Leaver-Fay, Andrew, O’Meara, Matthew J., Tyka, Mike, Jacak, Ron, Song, Yifan, Kellogg, Elizabeth H., Thompson, James, Davis, Ian W., Pache, Roland A., Lyskov, Sergey, Gray, Jeffrey J., Kortemme, Tanja, Richardson, Jane S., Havranek, James J., Snoeyink, Jack, Baker, David, Kuhlman, Brian
Publicado em 2013