Publications (59)
The Emergence of Scaling in Sequence-based Physical Models of Protein Evolution
Eric J. Deeds, Eugene I. Shakhnovich
Of sequence and structure: Strategies of protein thermostability in evolutionary perspective
Igor N. Berezovsky, Eugene I. Shakhnovich
The Error and Repair Catastrophes: A Two-Dimensional Phase Diagram in the Quasispecies Model
Emmanuel Tannenbaum, Eugene I. Shakhnovich
Graph's Topology and Free Energy of a Spin Model on the Graph
Jeong-Mo Choi, Amy I. Gilson, Eugene I. Shakhnovich
Identifying the protein folding nucleus using molecular dynamics
Nikolay V. Dokholyan, Sergey V. Buldyrev, H. Eugene Stanley +1
Structure-based prediction of protein-folding transition paths
William M. Jacobs, Eugene I. Shakhnovich
Excluded Volume in Protein Sidechain Packing
Edo Kussell, Jun Shimada, Eugene I. Shakhnovich
Positive and negative design in stability and thermal adaptation of natural proteins
Igor N. Berezovsky, Konstantin B. Zeldovich, Eugene I. Shakhnovich
The Importance of DNA Repair in Tumor Suppression
Yisroel Brumer, Eugene I. Shakhnovich
Phase diagram for unzipping DNA with long-range interactions
Eran A. Mukamel, Eugene I. Shakhnovich
Semiconservative Replication in the Quasispecies Model
Emmanuel Tannenbaum, Eric J. Deeds, Eugene I. Shakhnovich
An Analytical Approach to the Protein Designability Problem
Edo L. Kussell, Eugene I. Shakhnovich
Equilibrium Distribution of Mutators in the Single Fitness Peak Model
Emmanuel Tannenbaum, Eric Deeds, Eugene I. Shakhnovich
Emergence of species in evolutionary simulated annealing
Muyoung Heo, Louis Kang, Eugene I. Shakhnovich
High resolution protein folding with a transferable potential
Isaac A. Hubner, Eric J. Deeds, Eugene I. Shakhnovich
Protein Evolution within a Structural Space
Eric J. Deeds, Nikolay V. Dokholyan, Eugene I. Shakhnovich
Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition
Jingshan Zhang, Eugene I. Shakhnovich
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations
Shimon Bershtein, Wanmeng Mu, Eugene I. Shakhnovich
All-atom ab initio folding of a diverse set of proteins
Jae Shick Yang, William W. Chen, Jeffrey Skolnick +1
An Exact Model of Fluctuations in Gene Expression
William W. Chen, Jeremy L. England, Eugene I. Shakhnovich
Protein and DNA sequence determinants of thermophilic adaptation
Konstantin B. Zeldovich, Igor N. Berezovsky, Eugene I. Shakhnovich
Optimality of mutation and selection in germinal centers
Jingshan Zhang, Eugene I. Shakhnovich
Semiconservative replication in the quasispecies model II: Generalization to arbitrary lesion repair probabilities
Emmanuel Tannenbaum, James L. Sherley, Eugene I. Shakhnovich
Mode-coupling theory for heteropolymers
Estelle Pitard, Eugene I. Shakhnovich
Diversity against adversity: How adaptive immunity evolves potent antibodies
Muyoung Heo, Konstantin B. Zeldovich, Eugene I. Shakhnovich
Design of Proteins with Specified Thermal Properties
Michael P. Morrissey, Eugene I. Shakhnovich
The role of evolutionary selection in the dynamics of protein structure evolution
Amy I. Gilson, Ahmee Marshall-Christensen, Jeong-Mo Choi +1
Nucleation and the transition state of the SH3 domain
Isaac A. Hubner, Katherine A. Edmonds, Eugene I. Shakhnovich
Structural Determinant of Protein Designability
Jeremy L. England, Eugene I. Shakhnovich
An internal disulfide locks a misfolded aggregation-prone intermediate in cataract-linked mutants of human γD-crystallin
Eugene Serebryany, Jaie C. Woodard, Bharat V. Adkar +3
Absence of selection for quantum coherence in the Fenna-Matthews-Olson complex: a combined evolutionary and excitonic study
Stéphanie Valleau, Romain A. Studer, Florian Häse +5
Multi-scale sequence correlations increase proteome structural disorder and promiscuity
Ariel Afek, Eugene I. Shakhnovich, David B. Lukatsky
Thermal Adaptation in Viruses and Bacteria
Peiqiu Chen, Eugene I. Shakhnovich
A Structure-Centric View of Protein Evolution, Design and Adaptation
Eric J. Deeds, Eugene I. Shakhnovich
Evolutionary dynamics of adult stem cells: Comparison of random and immortal strand segregation mechanisms
Emmanuel Tannenbaum, James L. Sherley, Eugene I. Shakhnovich
Cooperativity and Stability in a Langevin Model of Protein Folding
Gabriel F. Berriz, Alexander M. Gutin, Eugene I. Shakhnovich
Discrete molecular dynamics studies of the folding of a protein-like model
Nikolay V. Dokholyan, Sergey V. Buldyrev, H. Eugene Stanley +1
Protein abundances and interactions coevolve to promote functional complexes while suppressing non-specific binding
Muyoung Heo, Sergei Maslov, Eugene I. Shakhnovich
Reversible stretching of homopolymers and random heteropolymers
Phillip L. Geissler, Eugene I. Shakhnovich
Emergence of clonal selection and affinity maturation in an ab initio microscopic model of immunity
Muyoung Heo, Konstantin B. Zeldovich, Eugene I. Shakhnovich
A simple physical model for scaling in protein-protein interaction networks
Eric J. Deeds, Orr Ashenberg, Eugene I. Shakhnovich
Sequence correlations shape protein promiscuity
David B. Lukatsky, Ariel Afek, Eugene I. Shakhnovich
Host-Parasite Co-evolution and Optimal Mutation Rates for Semi-conservative Quasispecies
Yisroel Brumer, Eugene I. Shakhnovich
Mechanical response of random heteropolymers
Phillip L. Geissler, Eugene I. Shakhnovich
Solution of the Quasispecies Model for an Arbitrary Gene Network
Emmanuel Tannenbaum, Eugene I. Shakhnovich
Sensitivity dependent model of protein-protein interaction networks
Jingshan Zhang, Eugene I. Shakhnovich
Understanding hierarchical protein evolution from first principles
Nikolay V. Dokholyan, Eugene I. Shakhnovich
Emergence of the protein universe in organismal evolution
Konstantin B. Zeldovich, Boris E. Shakhnovich, Eugene I. Shakhnovich
Emergence of mutationally robust proteins in a microscopic model of evolution
Konstantin B. Zeldovich, Eugene I. Shakhnovich
Understanding conserved amino acids in proteins
Nikolay V. Dokholyan, Leonid A. Mirny, Eugene I. Shakhnovich
Geometric and physical considerations for realistic protein models
Isaac A. Hubner, Eugene I. Shakhnovich
Thermodynamics of the Hairpin Ribozyme from All-Atom Simulations
Lucas G. Nivon, Eugene I. Shakhnovich
Imperfect DNA Repair and the Error Catastrophe
Yisroel Brumer, Emmanuel Tannenbaum, Eugene I. Shakhnovich
Entropic stabilization of proteins and its proteomic consequences
Igor N. Berezovsky, William W. Chen, Paul J. Choi +1
A Selective Advantage for Conservative Viruses
Yisroel Brumer, Eugene I. Shakhnovich
Lethal Mutagenesis in Viruses and Bacteria
Peiqiu Chen, Eugene I. Shakhnovich
Information and Protein Interfaces
William W. Chen, Paul J. Choi, Jason E. Donald +1
Thymic selection of T-cell receptors as an extreme value problem
Andrej Kosmrlj, Arup K. Chakraborty, Mehran Kardar +1
DNA unzipping phase diagram calculated via replica theory
C. Brian Roland, Kristi Adamson Hatch, Mara Prentiss +1