Eugene I. Shakhnovich

Publication Activity (10 Years)

Years Active: 1995-2020
Publications (10 Years): 6

Top Topics

Physicochemical Properties

Scoring Function

Protein Structure

Top Venues

PLoS Comput. Biol.

J. Comput. Chem.

Publications

David E. Graff, Eugene I. Shakhnovich, Connor W. Coley
Accelerating high-throughput virtual screening through molecular pool-based active learning. CoRR (2020)
Rostam M. Razban, Amy I Gilson, Niamh Durfee, Hendrik Strobelt, Kasper Dinkla, Jeong-Mo Choi, Hanspeter Pfister, Eugene I. Shakhnovich
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinform. 34 (20) (2018)
Rostam M. Razban, Amy I Gilson, Niamh Durfee, Hendrik Strobelt, Kasper Dinkla, Jeong-Mo Choi, Hanspeter Pfister, Eugene I. Shakhnovich
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes. Bioinform. 34 (23) (2018)
Nicolas Chéron, Eugene I. Shakhnovich
Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations. J. Comput. Chem. 38 (22) (2017)
Théau Debroise, Eugene I. Shakhnovich, Nicolas Chéron
A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016. J. Chem. Inf. Model. 57 (3) (2017)
Hugo Jacquin, Amy Gilson, Eugene I. Shakhnovich, Simona Cocco, Rémi Monasson
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models. PLoS Comput. Biol. 12 (5) (2016)
Jian Tian, Jaie C. Woodard, Anna Whitney, Eugene I. Shakhnovich
Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences. PLoS Comput. Biol. 11 (4) (2015)
Sílvia G. Estácio, Heinrich Krobath, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F. N. Faísca
-Microglobulin Amyloidogenic Behavior. PLoS Comput. Biol. 10 (5) (2014)
Murat Çetinbas, Eugene I. Shakhnovich
Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations. PLoS Comput. Biol. 9 (11) (2013)
Pouria Dasmeh, Adrian W. R. Serohijos, Kasper P. Kepp, Eugene I. Shakhnovich
Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability. PLoS Comput. Biol. 9 (3) (2013)
C. Scott Wylie, Eugene I. Shakhnovich
Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation. PLoS Comput. Biol. 8 (8) (2012)
Ranjan V. Mannige, Charles L. Brooks III, Eugene I. Shakhnovich
A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor. PLoS Comput. Biol. 8 (12) (2012)
Jingshan Zhang, Eugene I. Shakhnovich
Optimality of Mutation and Selection in Germinal Centers. PLoS Comput. Biol. 6 (6) (2010)
Muyoung Heo, Eugene I. Shakhnovich
Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response. PLoS Comput. Biol. 6 (3) (2010)
J. William Lee, Tomasz Zemojtel, Eugene I. Shakhnovich
Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes. J. Comput. Biol. 16 (2) (2009)
Jason E. Donald, Eugene I. Shakhnovich
SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Res. 37 (Database-Issue) (2009)
Peter S. Kutchukian, David Lou, Eugene I. Shakhnovich
Generation of Molecules Occupying Druglike Chemical Space. J. Chem. Inf. Model. 49 (7) (2009)
Konstantin B. Zeldovich, Igor N. Berezovsky, Eugene I. Shakhnovich
Protein and DNA Sequence Determinants of Thermophilic Adaptation. PLoS Comput. Biol. 3 (1) (2007)
Konstantin B. Zeldovich, Peiqiu Chen, Boris E. Shakhnovich, Eugene I. Shakhnovich
A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds. PLoS Comput. Biol. 3 (7) (2007)
Igor N. Berezovsky, Konstantin B. Zeldovich, Eugene I. Shakhnovich
Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins. PLoS Comput. Biol. 3 (3) (2007)
Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I. Shakhnovich
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. BMC Bioinform. 7 (2006)
Jason E. Donald, Eugene I. Shakhnovich
Determining functional specificity from protein sequences. Bioinform. 21 (11) (2005)
Jason E. Donald, Isaac A. Hubner, Veronica Rotemberg, Eugene I. Shakhnovich, Leonid A. Mirny
CoC: a database of universally conserved residues in protein folds. Bioinform. 21 (10) (2005)
Igor N. Berezovsky, William W. Chen, Paul J. Choi, Eugene I. Shakhnovich
Entropic Stabilization of Proteins and Its Proteomic Consequences. PLoS Comput. Biol. 1 (4) (2005)
Boris E. Shakhnovich, John M. Harvey, Steve Comeau, David Lorenz, Charles DeLisi, Eugene I. Shakhnovich
ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinform. 4 (2003)
C. Kissinger, A. Keith Dunker, Eugene I. Shakhnovich
Disorder in Protein Structure and Function - Session Introduction. Pacific Symposium on Biocomputing (1999)
Andrej Sali, Eugene I. Shakhnovich, Martin Karplus
Thermodynamics and kinetics of protein folding. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding (1995)