Eugene I. Shakhnovich

发表

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

David E. Graff, Eugene I. Shakhnovich, Connor W. Coley, 2020, Chemical science.

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

Eugene I. Shakhnovich, C. Scott Wylie, E. Shakhnovich, 2012, PLoS Comput. Biol..

CoC: a database of universally conserved residues in protein folds

Veronica Rotemberg, Eugene I. Shakhnovich, Leonid A. Mirny, 2005, Bioinform..

FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space

David Lou, Eugene I. Shakhnovich, Peter S. Kutchukian, 2009, J. Chem. Inf. Model..

Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences

Jian Tian, Eugene I. Shakhnovich, Jaie C. Woodard, 2015, PLoS Comput. Biol..

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

Eugene I. Shakhnovich, Jason E. Donald, E. Shakhnovich, 2008, Nucleic Acids Res..

The Evopopbot Chip: Ultra High-throughput Evolutionary Population Bottlenecking using Drop-Based Microfluidics

Ye Tao, Andrew B. Feldman, Eugene I. Shakhnovich, 2014 .

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

Eugene I. Shakhnovich, Murat Çetinbas, E. Shakhnovich, 2013, PLoS Comput. Biol..

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor

Charles L. Brooks, Eugene I. Shakhnovich, Ranjan V. Mannige, 2012, PLoS Comput. Biol..

Construction of Drug‐Like Compounds by Markov Chains

Eugen Lounkine, Meir Glick, Eugene I. Shakhnovich, 2013 .

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability

Adrian W. R. Serohijos, Eugene I. Shakhnovich, Adrian W. R. Serohijos, 2013, PLoS Comput. Biol..

Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins

Igor N. Berezovsky, Eugene I. Shakhnovich, Konstantin B. Zeldovich, 2006, PLoS Comput. Biol..

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

Simona Cocco, Rémi Monasson, Eugene I. Shakhnovich, 2015, bioRxiv.

Integrating computer-based de novo drug design and multidimensional filtering for desirable drugs

Sean Ekins, Eugene I. Shakhnovich, Carl Elkin, 2002 .

Determining functional specificity from protein sequences

Eugene I. Shakhnovich, Jason E. Donald, E. Shakhnovich, 2005, Bioinform..

Protein and DNA Sequence Determinants of Thermophilic Adaptation

Igor N. Berezovsky, Eugene I. Shakhnovich, Konstantin B. Zeldovich, 2006, PLoS Comput. Biol..

A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016

Eugene I. Shakhnovich, Théau Debroise, Nicolas Chéron, 2017, J. Chem. Inf. Model..

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

Eugene I. Shakhnovich, Muyoung Heo, E. Shakhnovich, 2009, PLoS Comput. Biol..

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

Hanspeter Pfister, Hendrik Strobelt, Eugene I. Shakhnovich, 2017, bioRxiv.

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes

Hanspeter Pfister, Hendrik Strobelt, Eugene I. Shakhnovich, 2018, Bioinform..

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

J. William Lee, Eugene I. Shakhnovich, Tomasz Zemojtel, 2009, J. Comput. Biol..

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds

Eugene I. Shakhnovich, Peiqiu Chen, Boris E. Shakhnovich, 2007, PLoS Comput. Biol..

ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations

Charles DeLisi, Eugene I. Shakhnovich, David Lorenz, 2003, BMC Bioinformatics.

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior

Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, 2014, PLoS Comput. Biol..

Entropic Stabilization of Proteins and Its Proteomic Consequences

Igor N. Berezovsky, Eugene I. Shakhnovich, William W. Chen, 2005, PLoS Comput. Biol..

PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

Dariusz Plewczynski, Marcin von Grotthuss, Leszek Rychlewski, 2006, BMC Bioinformatics.

Thermodynamics and kinetics of protein folding

Andrej Sali, Eugene I. Shakhnovich, Martin Karplus, 1995, Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding.

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

Eugene I. Shakhnovich, Nicolas Chéron, E. Shakhnovich, 2017, J. Comput. Chem..

Disorder in Protein Structure and Function - Session Introduction

A. Keith Dunker, Eugene I. Shakhnovich, C. Kissinger, 1999, Pacific Symposium on Biocomputing.

Optimality of Mutation and Selection in Germinal Centers

Eugene I. Shakhnovich, Jingshan Zhang, E. Shakhnovich, 2010, PLoS Comput. Biol..

Protein folding, evolution and design : Varenna on Lake Como, Villa Monastero, 11-21 July 2000

Guido Tiana, Eugene I. Shakhnovich, Ricardo A. Broglia, 2001 .

Enumeration of all compact conformations of copolymers with random sequence of links

Eugene I. Shakhnovich, E. Shakhnovich, A. Gutin, 1990 .

Predicting specificity-determining residues in two large eukaryotic transcription factor families

Eugene I. Shakhnovich, Jason E. Donald, E. Shakhnovich, 2005, Nucleic acids research.

Phase diagram of a model protein derived by exhaustive enumeration of the conformations

Aaron R. Dinner, Andrej Sali, Eugene I. Shakhnovich, 1994 .

Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus

Eugene I. Shakhnovich, Leonid A. Mirny, L. Mirny, 2000, Nature Structural Biology.

networks From The Cover : A simple physical model for scaling in protein-protein interaction

Eric J. Deeds, Eugene I. Shakhnovich, Orr Ashenberg, 2009 .

Influenza A H1N1 Pandemic Strain Evolution – Divergence and the Potential for Antigenic Drift Variants

Eugene I. Shakhnovich, Adrian W. R. Serohijos, Andrew Pekosz, 2014, PloS one.

Development of a Knowledge-Based Potential for Crystals of Small Organic Molecules: Calculation of Energy Surfaces for C)0‚‚‚H-N Hydrogen Bonds

Eugene I. Shakhnovich, Bartosz A. Grzybowski, Alexey V. Ishchenko, 2000 .

Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations

Eugene I. Shakhnovich, Victor Abkevich, E. Shakhnovich, 1994 .

Evidence of evolutionary selection for cotranslational folding

Eugene I. Shakhnovich, William M. Jacobs, E. Shakhnovich, 2017, Proceedings of the National Academy of Sciences.

Growth tradeoffs produce complex microbial communities on a single limiting resource

Michael Manhart, Eugene I. Shakhnovich, 2018 .

In SilicoFragment-Based Generation of Drug-Like Compounds

David Lou, Eugene I. Shakhnovich, Peter S. Kutchukian, 2011 .

On the role of conformational geometry in protein folding

Vijay S. Pande, Alexander Y. Grosberg, Eugene I. Shakhnovich, 1999 .

Contribution of Selection for Protein Folding Stability in Shaping the Patterns of Polymorphisms in Coding Regions

Eugene I. Shakhnovich, Adrian W. R. Serohijos, E. Shakhnovich, 2013, Molecular biology and evolution.

Protein stability imposes limits on organism complexity and speed of molecular evolution

Eugene I. Shakhnovich, Konstantin B. Zeldovich, E. Shakhnovich, 2007, Proceedings of the National Academy of Sciences.

Semiconservative replication, genetic repair, and many-gened genomes: Extending the quasispecies paradigm to living systems

Emmanuel Tannenbaum, Eugene I. Shakhnovich, E. Shakhnovich, 2005 .

Statistical mechanics of polymers with distance constraints

Eugene I. Shakhnovich, E. Shakhnovich, A. Gutin, 1994 .

Natural selection of more designable folds: A mechanism for thermophilic adaptation

Eugene I. Shakhnovich, Jeremy L. England, Boris E. Shakhnovich, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Ground state of random copolymers and the discrete random energy model

Eugene I. Shakhnovich, E. Shakhnovich, A. Gutin, 1993 .

Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition

Andrej Sali, Eugene I. Shakhnovich, Martin Karplus, 1998 .

Frozen states of a disordered globular heteropolymer

Eugene I. Shakhnovich, E. Shakhnovich, A. Gutin, 1989 .

SMOG : DE NOVO DESIGN METHOD BASED ON SIMPLE, FAST, AND ACCURATE FREE ENERGY ESTIMATES. 2. CASE STUDIES IN MOLECULAR DESIGN

Eugene I. Shakhnovich, E. Shakhnovich, R. Dewitte, 1997 .

Protein folding, evolution and design

Guido Tiana, Eugene I. Shakhnovich, Ricardo A. Broglia, 2001 .

Relaxation to Equilibrium in the Random Energy Model

Eugene I. Shakhnovich, A. M. Gutin, 1989 .