Eugene I. Shakhnovich

27 papers Misc 1Journal 25Unranked 1
YearRankTypeTitle / Venue / Authors
2020 J jnl
Accelerating high-throughput virtual screening through molecular pool-based active learning.
CoRR
David E. Graff, Eugene I. Shakhnovich, Connor W. Coley
2018 J jnl
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.
Bioinform.
Rostam M. Razban, Amy I Gilson, Niamh Durfee, Hendrik Strobelt, Kasper Dinkla, Jeong-Mo Choi, Hanspeter Pfister, Eugene I. Shakhnovich
2018 J jnl
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.
Bioinform.
Rostam M. Razban, Amy I Gilson, Niamh Durfee, Hendrik Strobelt, Kasper Dinkla, Jeong-Mo Choi, Hanspeter Pfister, Eugene I. Shakhnovich
2017 J jnl
A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016.
J. Chem. Inf. Model.
Théau Debroise, Eugene I. Shakhnovich, Nicolas Chéron
2017 J jnl
Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations.
J. Comput. Chem.
Nicolas Chéron, Eugene I. Shakhnovich
2016 J jnl
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.
PLoS Comput. Biol.
Hugo Jacquin, Amy Gilson, Eugene I. Shakhnovich, Simona Cocco, Rémi Monasson
2015 J jnl
Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences.
PLoS Comput. Biol.
Jian Tian, Jaie C. Woodard, Anna Whitney, Eugene I. Shakhnovich
2014 J jnl
A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β
PLoS Comput. Biol.
Sílvia G. Estácio, Heinrich Krobath, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F. N. Faísca
2013 J jnl
Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations.
PLoS Comput. Biol.
Murat Çetinbas, Eugene I. Shakhnovich
2013 J jnl
Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability.
PLoS Comput. Biol.
Pouria Dasmeh, Adrian W. R. Serohijos, Kasper P. Kepp, Eugene I. Shakhnovich
2012 J jnl
A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor.
PLoS Comput. Biol.
Ranjan V. Mannige, Charles L. Brooks III, Eugene I. Shakhnovich
2012 J jnl
Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation.
PLoS Comput. Biol.
C. Scott Wylie, Eugene I. Shakhnovich
2010 J jnl
Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response.
PLoS Comput. Biol.
Muyoung Heo, Eugene I. Shakhnovich
2010 J jnl
Optimality of Mutation and Selection in Germinal Centers.
PLoS Comput. Biol.
Jingshan Zhang, Eugene I. Shakhnovich
2009 J jnl
FOG: Fragment Optimized Growth Algorithm for the
J. Chem. Inf. Model.
Peter S. Kutchukian, David Lou, Eugene I. Shakhnovich
2009 J jnl
SDR: a database of predicted specificity-determining residues in proteins.
Nucleic Acids Res.
Jason E. Donald, Eugene I. Shakhnovich
2009 J jnl
Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes.
J. Comput. Biol.
J. William Lee, Tomasz Zemojtel, Eugene I. Shakhnovich
2007 J jnl
A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds.
PLoS Comput. Biol.
Konstantin B. Zeldovich, Peiqiu Chen, Boris E. Shakhnovich, Eugene I. Shakhnovich
2007 J jnl
Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins.
PLoS Comput. Biol.
Igor N. Berezovsky, Konstantin B. Zeldovich, Eugene I. Shakhnovich
2007 J jnl
Protein and DNA Sequence Determinants of Thermophilic Adaptation.
PLoS Comput. Biol.
Konstantin B. Zeldovich, Igor N. Berezovsky, Eugene I. Shakhnovich
2006 J jnl
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
BMC Bioinform.
Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I. Shakhnovich
2005 J jnl
CoC: a database of universally conserved residues in protein folds.
Bioinform.
Jason E. Donald, Isaac A. Hubner, Veronica Rotemberg, Eugene I. Shakhnovich, Leonid A. Mirny
2005 J jnl
Determining functional specificity from protein sequences.
Bioinform.
Jason E. Donald, Eugene I. Shakhnovich
2005 J jnl
Entropic Stabilization of Proteins and Its Proteomic Consequences.
PLoS Comput. Biol.
Igor N. Berezovsky, William W. Chen, Paul J. Choi, Eugene I. Shakhnovich
2003 J jnl
ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations.
BMC Bioinform.
Boris E. Shakhnovich, John M. Harvey, Steve Comeau, David Lorenz, Charles DeLisi, Eugene I. Shakhnovich
1999 Misc conf
Disorder in Protein Structure and Function - Session Introduction.
Pacific Symposium on Biocomputing
C. Kissinger, A. Keith Dunker, Eugene I. Shakhnovich
1995 — conf
Thermodynamics and kinetics of protein folding.
Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding
Andrej Sali, Eugene I. Shakhnovich, Martin Karplus