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Yifan Song, Ph.D. - Publications

Affiliations: 
2006 City University of New York, New York, NY, United States 
Area:
General Biophysics, Molecular Physics
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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, ... ... Song Y, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.557
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  0.605
2016 Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen PJ, Rocklin GJ, Song Y, et al. Accurate de novo design of hyperstable constrained peptides. Nature. PMID 27626386 DOI: 10.1038/Nature19791  0.728
2016 Thyme S, Song Y. Computational Design of DNA-Binding Proteins. Methods in Molecular Biology (Clifton, N.J.). 1414: 265-83. PMID 27094297 DOI: 10.1007/978-1-4939-3569-7_16  0.725
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  0.547
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  0.648
2015 Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW, Baker D, Stevens RC, Schultz PG. Transition states. Trapping a transition state in a computationally designed protein bottle. Science (New York, N.Y.). 347: 863-7. PMID 25700516 DOI: 10.1126/Science.Aaa2424  0.7
2014 Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Research. 42: 13839-52. PMID 25389263 DOI: 10.1093/Nar/Gku1096  0.752
2014 Song Y, Gunner MR. Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions. Proceedings of the National Academy of Sciences of the United States of America. 111: 16377-82. PMID 25362051 DOI: 10.1073/Pnas.1411119111  0.601
2014 Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, et al. A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell. 157: 1644-56. PMID 24949974 DOI: 10.1016/J.Cell.2014.04.034  0.398
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  0.488
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  0.704
2013 Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0  0.704
2012 Lange OF, Rossi P, Sgourakis NG, Song Y, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT, Baker D. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proceedings of the National Academy of Sciences of the United States of America. 109: 10873-8. PMID 22733734 DOI: 10.1073/Pnas.1203013109  0.672
2012 Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, Myers CA, Kamisetty H, Blair P, Wilson IA, Baker D. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nature Biotechnology. 30: 543-8. PMID 22634563 DOI: 10.1038/Nbt.2214  0.437
2012 Khare SD, Kipnis Y, Greisen P, Takeuchi R, Ashani Y, Goldsmith M, Song Y, Gallaher JL, Silman I, Leader H, Sussman JL, Stoddard BL, Tawfik DS, Baker D. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nature Chemical Biology. 8: 294-300. PMID 22306579 DOI: 10.1038/Nchembio.777  0.603
2011 Song Y. Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol. Proteins. 79: 3356-63. PMID 22072519 DOI: 10.1002/Prot.23146  0.347
2011 Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Structure-guided forcefield optimization. Proteins. 79: 1898-909. PMID 21488100 DOI: 10.1002/Prot.23013  0.74
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  0.461
2009 Song Y, Gunner MR. Using multiconformation continuum electrostatics to compare chloride binding motifs in alpha-amylase, human serum albumin, and Omp32. Journal of Molecular Biology. 387: 840-56. PMID 19340943 DOI: 10.1016/J.Jmb.2009.01.038  0.604
2009 Song Y, Mao J, Gunner MR. MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling. Journal of Computational Chemistry. 30: 2231-47. PMID 19274707 DOI: 10.1002/Jcc.21222  0.628
2006 Gunner MR, Mao J, Song Y, Kim J. Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations. Biochimica Et Biophysica Acta. 1757: 942-68. PMID 16905113 DOI: 10.1016/J.Bbabio.2006.06.005  0.625
2006 Song Y, Michonova-Alexova E, Gunner MR. Calculated proton uptake on anaerobic reduction of cytochrome C oxidase: is the reaction electroneutral? Biochemistry. 45: 7959-75. PMID 16800622 DOI: 10.1021/Bi052183D  0.602
2006 Song Y, Mao J, Gunner MR. Electrostatic environment of hemes in proteins: pK(a)s of hydroxyl ligands. Biochemistry. 45: 7949-58. PMID 16800621 DOI: 10.1021/Bi052182L  0.606
2003 Song Y, Mao J, Gunner MR. Calculation of proton transfers in Bacteriorhodopsin bR and M intermediates. Biochemistry. 42: 9875-88. PMID 12924936 DOI: 10.1021/Bi034482D  0.609
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