Eugene I. Shakhnovich

According to our database, Eugene I. Shakhnovich authored at least 26 papers between 1995 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2020

Accelerating high-throughput virtual screening through molecular pool-based active learning.

David E. Graff, Eugene I. Shakhnovich, Connor W. Coley

CoRR, 2020

2018

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

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

Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations.

Nicolas Chéron, Eugene I. Shakhnovich

J. Comput. Chem., 2017

2016

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

2015

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

2014

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

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

Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations.

Murat Çetinbas, Eugene I. Shakhnovich

PLoS Comput. Biol., 2013

2012

Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation.

C. Scott Wylie, Eugene I. Shakhnovich

PLoS Comput. Biol., 2012

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

2010

Optimality of Mutation and Selection in Germinal Centers.

Jingshan Zhang, Eugene I. Shakhnovich

PLoS Comput. Biol., 2010

Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response.

Muyoung Heo, Eugene I. Shakhnovich

PLoS Comput. Biol., 2010

2009

SDR: a database of predicted specificity-determining residues in proteins.

Jason E. Donald, Eugene I. Shakhnovich

Nucleic Acids Res., 2009

FOG: Fragment Optimized Growth Algorithm for the <i>de Novo</i> Generation of Molecules Occupying Druglike Chemical Space.

Peter S. Kutchukian, David Lou, Eugene I. Shakhnovich

J. Chem. Inf. Model., 2009

Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes.

J. William Lee, Tomasz Zemojtel, Eugene I. Shakhnovich

J. Comput. Biol., 2009

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

Protein and DNA Sequence Determinants of Thermophilic Adaptation.

Konstantin B. Zeldovich, Igor N. Berezovsky, Eugene I. Shakhnovich

PLoS Comput. Biol., 2007

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

2006

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

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

Determining functional specificity from protein sequences.

Jason E. Donald, Eugene I. Shakhnovich

Bioinform., 2005

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

2003

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

1999

Disorder in Protein Structure and Function - Session Introduction.

C. Kissinger, A. Keith Dunker, Eugene I. Shakhnovich

Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

1995

Thermodynamics and kinetics of protein folding.

Andrej Sali, Eugene I. Shakhnovich, Martin Karplus

Proceedings of the Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995