Thermodynamics and kinetics of protein folding. - Andrej Sali; Eugene I. Shakhnovich; Martin Karplus (Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995)

Disorder in Protein Structure and Function - Session Introduction. - C. Kissinger; A. Keith Dunker; Eugene I. Shakhnovich (Pacific Symposium on Biocomputing, 1999)

ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations. - Boris E. Shakhnovich; John M. Harvey; Steve Comeau; David Lorenz; Charles DeLisi; Eugene I. Shakhnovich (BMC Bioinform., 2003)

CoC: a database of universally conserved residues in protein folds. - Jason E. Donald; Isaac A. Hubner; Veronica Rotemberg; Eugene I. Shakhnovich; Leonid A. Mirny (Bioinform., 2005)

Determining functional specificity from protein sequences. - Jason E. Donald; Eugene I. Shakhnovich (Bioinform., 2005)

Entropic Stabilization of Proteins and Its Proteomic Consequences. - Igor N. Berezovsky; William W. Chen; Paul J. Choi; Eugene I. Shakhnovich (PLoS Comput. Biol., 2005)

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. - Marcin von Grotthuss; Dariusz Plewczynski; Krzysztof Ginalski; Leszek Rychlewski; Eugene I. Shakhnovich (BMC Bioinform., 2006)

Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins. - Igor N. Berezovsky; Konstantin B. Zeldovich; Eugene I. Shakhnovich (PLoS Comput. Biol., 2007)

Protein and DNA Sequence Determinants of Thermophilic Adaptation. - Konstantin B. Zeldovich; Igor N. Berezovsky; Eugene I. Shakhnovich (PLoS Comput. Biol., 2007)

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds. - Konstantin B. Zeldovich; Peiqiu Chen; Boris E. Shakhnovich; Eugene I. Shakhnovich (PLoS Comput. Biol., 2007)

Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes. - J. William Lee; Tomasz Zemojtel; Eugene I. Shakhnovich (J. Comput. Biol., 2009)

FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space. - Peter S. Kutchukian; David Lou; Eugene I. Shakhnovich (J. Chem. Inf. Model., 2009)

SDR: a database of predicted specificity-determining residues in proteins. - Jason E. Donald; Eugene I. Shakhnovich (Nucleic Acids Res., 2009)

Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response. - Muyoung Heo; Eugene I. Shakhnovich (PLoS Comput. Biol., 2010)

Optimality of Mutation and Selection in Germinal Centers. - Jingshan Zhang; Eugene I. Shakhnovich (PLoS Comput. Biol., 2010)

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor. - Ranjan V. Mannige; Charles L. Brooks III; Eugene I. Shakhnovich (PLoS Comput. Biol., 2012)

Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation. - C. Scott Wylie; Eugene I. Shakhnovich (PLoS Comput. Biol., 2012)

Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations. - Murat Çetinbas; Eugene I. Shakhnovich (PLoS Comput. Biol., 2013)

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability. - Pouria Dasmeh; Adrian W. R. Serohijos; Kasper P. Kepp; Eugene I. Shakhnovich (PLoS Comput. Biol., 2013)

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior. - Sílvia G. Estácio; Heinrich Krobath; Diogo Vila-Viçosa; Miguel Machuqueiro; Eugene I. Shakhnovich; Patrícia F. N. Faísca (PLoS Comput. Biol., 2014)

Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences. - Jian Tian; Jaie C. Woodard; Anna Whitney; Eugene I. Shakhnovich (PLoS Comput. Biol., 2015)

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models. - Hugo Jacquin; Amy Gilson; Eugene I. Shakhnovich; Simona Cocco; Rémi Monasson (PLoS Comput. Biol., 2016)

Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations. - Nicolas Chéron; Eugene I. Shakhnovich (J. Comput. Chem., 2017)

A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016. - Théau Debroise; Eugene I. Shakhnovich; Nicolas Chéron (J. Chem. Inf. Model., 2017)

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. - Rostam M. Razban; Amy I Gilson; Niamh Durfee; Hendrik Strobelt; Kasper Dinkla; Jeong-Mo Choi; Hanspeter Pfister; Eugene I. Shakhnovich (Bioinform., 2018)

Accelerating high-throughput virtual screening through molecular pool-based active learning. - David E. Graff; Eugene I. Shakhnovich; Connor W. Coley (CoRR, 2020)