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Physical Biology|March 16, 2013
A one-shot germinal center model under protein structural stability constraintsSana Raoof, Muyoung Heo, Eugene I ShakhnovichNature Communications|June 15, 2022
Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potentialSimon Axelrod, Eugene Shakhnovich, Rafael Gómez-BombarelliPlos Computational Biology|November 16, 2020
Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteinsAmir Bitran, William M Jacobs, Eugene ShakhnovichMolecular Systems Biology|August 7, 2008
Constraints imposed by non-functional protein-protein interactions on gene expression and proteome sizeJingshan Zhang, Sergei Maslov, Eugene I ShakhnovichProceedings of the National Academy of Sciences of the United States of America|January 24, 2009
Emergence of species in evolutionary "simulated annealing"Muyoung Heo, Louis Kang, Eugene I ShakhnovichJournal of Medicinal Chemistry|September 11, 2015
OpenGrowth: An Automated and Rational Algorithm for Finding New Protein LigandsNicolas Chéron, Naveen Jasty, Eugene I ShakhnovichProteins|March 3, 2011
The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potentialJiabin Xu, Lei Huang, Eugene I ShakhnovichJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|February 6, 2009
Systems-level evidence of transcriptional co-regulation of yeast protein complexesJ William Lee, Tomasz Zemojtel, Eugene ShakhnovichProteins|July 2, 2003
Side-chain dynamics and protein foldingEdo Kussell, Jun Shimada, Eugene I ShakhnovichJournal of Molecular Biology|July 27, 2001
Excluded volume in protein side-chain packingE Kussell, J Shimada, E I ShakhnovichPageof 47