Eugene I. Shakhnovich

Eugene I. Shakhnovich's AcademicInfluence.com Rankings

Chemistry

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Chemistry

Eugene I. Shakhnovich's Degrees

Bachelors Chemistry University of California, Berkeley

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Eugene I. Shakhnovich's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

How does a protein fold? (1994) (816)
Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. (1994) (500)
Engineering of stable and fast-folding sequences of model proteins. (1993) (470)
Specific nucleus as the transition state for protein folding: evidence from the lattice model. (1994) (434)
Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. (1999) (399)
The role of topological constraints in the kinetics of collapse of macromolecules (1988) (338)
Protein folding theory: from lattice to all-atom models. (2001) (332)
Theoretical studies of protein-folding thermodynamics and kinetics. (1997) (323)
Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. (2006) (312)
Estimating the Entropic Cost of Self-Assembly of Multiparticle Hydrogen-Bonded Aggregates Based on the Cyanuric Acid·Melamine Lattice (1998) (310)
Conserved residues and the mechanism of protein folding (1996) (298)
Discrete molecular dynamics studies of the folding of a protein-like model. (1998) (287)
A test of lattice protein folding algorithms. (1995) (283)
Topological determinants of protein folding (2002) (276)
How to derive a protein folding potential? A new approach to an old problem. (1996) (251)
Protein and DNA Sequence Determinants of Thermophilic Adaptation (2006) (247)
Physics and evolution of thermophilic adaptation. (2005) (247)
Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. (1989) (244)
Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. (1995) (240)
Protein stability imposes limits on organism complexity and speed of molecular evolution (2007) (239)
SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence (1996) (225)
A new approach to the design of stable proteins. (1993) (207)
Implications of thermodynamics of protein folding for evolution of primary sequences (1990) (200)
Enumeration of all compact conformations of copolymers with random sequence of links (1990) (198)
On the origin and highly likely completeness of single-domain protein structures. (2006) (184)
Common activation mechanism of class A GPCRs (2019) (181)
Expanding protein universe and its origin from the biological Big Bang (2002) (180)
A biophysical protein folding model accounts for most mutational fitness effects in viruses (2011) (178)
How evolution makes proteins fold quickly. (1998) (177)
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation (2002) (171)
The interface of protein structure, protein biophysics, and molecular evolution (2012) (171)
Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations (1994) (168)
Understanding hierarchical protein evolution from first principles. (2001) (164)
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. (2002) (157)
Protein design: a perspective from simple tractable models. (1998) (149)
Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness. (2013) (148)
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus (2000) (147)
Identifying the protein folding nucleus using molecular dynamics. (1998) (144)
The folding mechanics of a knotted protein. (2006) (142)
Is burst hydrophobic collapse necessary for protein folding? (1995) (141)
The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. (2000) (139)
Evidence for the role of PrP(C) helix 1 in the hydrophilic seeding of prion aggregates. (1999) (132)
Evolutionary conservation of the folding nucleus. (2000) (131)
SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. (2002) (128)
Evolution-like selection of fast-folding model proteins. (1995) (127)
Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins (2006) (121)
Direct molecular dynamics observation of protein folding transition state ensemble. (2002) (121)
Biophysical principles predict fitness landscapes of drug resistance (2016) (119)
Structural similarity enhances interaction propensity of proteins. (2006) (118)
Structural determinant of protein designability. (2002) (107)
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations (2011) (106)
What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis. (2000) (105)
Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. (1996) (103)
Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size (2008) (101)
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations (2001) (100)
A simple physical model for scaling in protein-protein interaction networks. (2005) (98)
All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples. (2009) (98)
Protein biophysics explains why highly abundant proteins evolve slowly. (2012) (97)
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions (2011) (94)
Using a Convenient, Quantitative Model for Torsional Entropy To Establish Qualitative Trends for Molecular Processes That Restrict Conformational Freedom (1998) (94)
Frozen states of a disordered globular heteropolymer (1989) (93)
All-atom ab initio folding of a diverse set of proteins. (2006) (90)
Natural selection of more designable folds: A mechanism for thermophilic adaptation (2003) (89)
Entropic Stabilization of Proteins and Its Proteomic Consequences (2005) (85)
Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases (2003) (85)
Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics. (2014) (83)
De novo design: balancing novelty and confined chemical space (2010) (81)
Protein structure and evolutionary history determine sequence space topology. (2004) (81)
Formation of microdomains in a quenched disordered heteropolymer (1989) (81)
Understanding ensemble protein folding at atomic detail (2006) (80)
Evidence of evolutionary selection for cotranslational folding (2017) (79)
A structure-based method for derivation of all-atom potentials for protein folding (2002) (79)
Robust protein–protein interactions in crowded cellular environments (2007) (79)
Pseudodihedrals: Simplified protein backbone representation with knowledge‐based energy (1994) (78)
Kinetics of protein folding (1995) (76)
Combinatorial computational method gives new picomolar ligands for a known enzyme (2002) (76)
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. (2005) (74)
Understanding protein evolution: from protein physics to Darwinian selection. (2008) (74)
Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria (2015) (73)
Ground state of random copolymers and the discrete random energy model (1993) (71)
Commitment and nucleation in the protein G transition state. (2004) (70)
FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space (2009) (68)
SMOG : DE NOVO DESIGN METHOD BASED ON SIMPLE, FAST, AND ACCURATE FREE ENERGY ESTIMATES. 2. CASE STUDIES IN MOLECULAR DESIGN (1997) (66)
Modeling protein folding: the beauty and power of simplicity. (1996) (66)
Improved design of stable and fast-folding model proteins. (1996) (66)
Universality and diversity of folding mechanics for three-helix bundle proteins (2007) (65)
Identification of the minimal protein-folding nucleus through loop-entropy perturbations. (2006) (65)
A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds (2007) (62)
Folding and misfolding of designed proteinlike chains with mutations (1997) (61)
Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. (2004) (60)
Temperature dependence of the folding rate in a simple protein model: Search for a “glass” transition (1998) (60)
Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations. (2017) (60)
Accelerating high-throughput virtual screening through molecular pool-based active learning† (2020) (59)
Protein structure prediction by threading. Why it works and why it does not. (1998) (59)
Energetics of protein–DNA interactions (2006) (58)
Differential Enzyme Flexibility Probed Using Solid-State Nanopores. (2018) (58)
Functional fingerprints of folds: evidence for correlated structure-function evolution. (2003) (57)
Lethal Mutagenesis in Viruses and Bacteria (2009) (55)
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. (2002) (55)
Dynamic metastable long-living droplets formed by sticker-spacer proteins (2020) (54)
Collapse of unfolded proteins in a mixture of denaturants. (2012) (54)
Statistically enhanced self-attraction of random patterns. (2006) (52)
Design of proteins with selected thermal properties. (1996) (52)
The Nonergodic (“Spin-Glass–Like”) Phase of Heteropolymer with Quenched Disordered Sequence of Links (1989) (52)
Imprint of evolution on protein structures. (2004) (51)
Optimality of Mutation and Selection in Germinal Centers (2010) (51)
Accessibility of the Shine–Dalgarno sequence dictates N-terminal codon bias in E. coli (2017) (51)
A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies. (1998) (51)
Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity (2016) (51)
High-resolution protein folding with a transferable potential. (2005) (50)
Nucleation and the transition state of the SH3 domain. (2005) (50)
Contribution of Selection for Protein Folding Stability in Shaping the Patterns of Polymorphisms in Coding Regions (2013) (49)
Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential. (2004) (49)
Hiking in the energy landscape in sequence space: A bumpy road to good folders (1999) (49)
Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability (2013) (49)
Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model. (2001) (46)
Thermal adaptation of viruses and bacteria. (2009) (46)
Thymic selection of T-cell receptors as an extreme value problem. (2009) (46)
Folding nucleus: specific or multiple? Insights from lattice models and experiments. (1998) (45)
Non‐native interactions play an effective role in protein folding dynamics (2010) (44)
OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. (2016) (43)
An Internal Disulfide Locks a Misfolded Aggregation-prone Intermediate in Cataract-linked Mutants of Human γD-Crystallin* (2016) (43)
Different circular permutations produced different folding nuclei in proteins: a computational study. (2001) (43)
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models (2015) (43)
Phase diagram of a model protein derived by exhaustive enumeration of the conformations (1994) (42)
Prokaryotic phylogenies inferred from protein structural domains. (2005) (41)
Genetic instability and the quasispecies model. (2006) (41)
Factors that affect the folding ability of proteins (1998) (41)
Influenza A H1N1 Pandemic Strain Evolution – Divergence and the Potential for Antigenic Drift Variants (2014) (40)
From knowledge-based potentials to combinatorial lead design in silico. (2002) (40)
Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants. (2012) (40)
Simulation study of the collapse of linear and ring homopolymers (1995) (40)
Excluded volume in protein side-chain packing. (2001) (39)
The Influence of Selection for Protein Stability on dN/dS Estimations (2014) (39)
Polymers with annealed and quenched branchings belong to different universality classes (1993) (38)
Relaxation to Equilibrium in the Random Energy Model (1989) (38)
Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship. (2015) (38)
Development of a Knowledge-Based Potential for Crystals of Small Organic Molecules: Calculation of Energy Surfaces for C)0‚‚‚H-N Hydrogen Bonds (2000) (38)
Domains in folding of model proteins (1995) (38)
How the first biopolymers could have evolved. (1996) (37)
STATISTICAL MECHANICS OF RANDOM HETEROPOLYMERS (1997) (37)
Simulations of chaperone-assisted folding. (1996) (37)
Theory of kinetic partitioning in protein folding with possible applications to prions (1998) (37)
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics (2006) (36)
Protein evolution within a structural space. (2003) (36)
Dynamic disulfide exchange in a crystallin protein in the human eye lens promotes cataract-associated aggregation (2018) (36)
A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. (1998) (36)
Optimization of lag phase shapes the evolution of a bacterial enzyme (2016) (36)
Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score (2000) (33)
A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior (2014) (33)
Lessons from the design of a novel atomic potential for protein folding (2005) (33)
Recognition between random heteropolymers and multifunctional disordered surfaces (1997) (32)
Predicting specificity-determining residues in two large eukaryotic transcription factor families (2005) (32)
Physical origins of protein superfamilies. (2005) (32)
The role of cotranslation in protein folding: a lattice model study (2004) (32)
On the role of conformational geometry in protein folding (1999) (31)
Semiconservative replication, genetic repair, and many-gened genomes: Extending the quasispecies paradigm to living systems (2005) (31)
Highly abundant proteins favor more stable 3D structures in yeast. (2013) (30)
Common motifs and topological effects in the protein folding transition state. (2006) (29)
The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential. (2007) (29)
Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak (2019) (29)
Solution of the quasispecies model for an arbitrary gene network. (2004) (29)
Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps. (2010) (29)
Folding by association (1999) (29)
STABILITY OF DESIGNED PROTEINS AGAINST MUTATIONS (1998) (28)
Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps (2020) (28)
Analysis of knowledge‐based protein‐ligand potentials using a self‐consistent method (2008) (28)
Robustness of atomistic Gō models in predicting native-like folding intermediates. (2012) (28)
Statistical significance of protein structure prediction by threading. (2000) (28)
Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences (2015) (27)
Folding kinetics of villin 14T, a protein domain with a central beta-sheet and two hydrophobic cores. (1998) (27)
Growth tradeoffs produce complex microbial communities on a single limiting resource (2018) (27)
Statistical mechanics of polymers with distance constraints (1994) (27)
Structural and energetic determinants of co-translational folding. (2013) (27)
Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics (2018) (27)
The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution. (2016) (27)
Influence of point mutations on protein structure: probability of a neutral mutation. (1991) (26)
Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation (2012) (26)
Using protein design for homology detection and active site searches (2003) (26)
Tradeoffs between microbial growth phases lead to frequency-dependent and non-transitive selection (2016) (26)
Adsorption of random copolymers on disordered surfaces (1998) (25)
Differential stabilization of two hydrophobic cores in the transition state of the villin 14T folding reaction. (2000) (25)
Evolution on the Biophysical Fitness Landscape of an RNA Virus (2016) (25)
Identifying importance of amino acids for protein folding from crystal structures. (2003) (25)
A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016 (2017) (24)
A knowledge‐based move set for protein folding (2006) (24)
[The theory of cooperative transitions in protein globules]. (1982) (24)
Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics (2015) (24)
The structure of a random heteropolymer in a disordered medium: Ensemble growth simulation (1997) (24)
Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms. (2004) (23)
Equilibrium distribution of mutators in the single fitness peak model. (2003) (23)
A structure-centric view of protein evolution, design, and adaptation. (2006) (23)
Microphase Ordering in Melts of Randomly Grafted Copolymers (1999) (22)
All-atom Monte Carlo simulation of GCAA RNA folding. (2004) (22)
Searching the Sequence Space for Potent Aptamers Using SELEX in Silico. (2015) (22)
Repurposing of rutin for the inhibition of norovirus replication (2015) (22)
Evolution of specificity in protein-protein interactions. (2014) (22)
Emergence of species in evolutionary “simulated annealing” (2008) (21)
Cooperativity and stability in a Langevin model of proteinlike folding (1996) (21)
Reversible stretching of random heteropolymers. (2001) (21)
Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis. (2008) (21)
Semiconservative replication in the quasispecies model. (2003) (21)
Side‐chain dynamics and protein folding (2001) (21)
Proteomic traces of speciation. (2004) (20)
Structure-Based Prediction of Protein-Folding Transition Paths (2016) (20)
Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants. (2017) (20)
Determining functional specificity from protein sequences (2005) (20)
Phase behavior of random copolymers in quenched random media (1995) (20)
SDR: a database of predicted specificity-determining residues in proteins (2008) (19)
Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases. (2019) (18)
A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor (2012) (18)
ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations (2003) (18)
[The role of topological limitations in the kinetics of homopolymer collapse and self-assembly of biopolymers]. (1988) (18)
The ensemble folding kinetics of the FBP28 WW domain revealed by an all‐atom Monte Carlo simulation in a knowledge‐based potential (2011) (18)
Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations (2013) (18)
Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response (2009) (18)
Is there an en route folding intermediate for cold shock proteins? (2012) (17)
Understanding conserved amino acids in proteins (2000) (17)
Error and repair catastrophes: A two-dimensional phase diagram in the quasispecies model. (2003) (17)
Assessing the Effect of Loop Mutations in the Folding Space of β2-Microglobulin with Molecular Dynamics Simulations (2013) (16)
Effect of sampling on BACE‐1 ligands binding free energy predictions via MM‐PBSA calculations (2017) (16)
Integrating computer-based de novo drug design and multidimensional filtering for desirable drugs (2002) (16)
Native atom types for knowledge-based potentials: application to binding energy prediction. (2004) (16)
Protein folding: To knot or not to knot? (2011) (15)
Statistically enhanced promiscuity of structurally correlated patterns. (2008) (15)
Phase separation of a binary fluid containing surfactants in a Hele-Shaw cell (1999) (15)
Mode-coupling theory for heteropolymers. (1999) (14)
Computer simulations of prebiotic evolution. (1997) (14)
Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding. (2015) (14)
Conformational Entropy of a Branched Polymer (1995) (14)
Mechanical response of random heteropolymers (2001) (14)
Fluctuation effects on microphase separation in random copolymers (1994) (14)
Evolutionary dynamics of viral escape under antibodies stress: A biophysical model (2016) (13)
Multi-scale sequence correlations increase proteome structural disorder and promiscuity. (2010) (13)
[Protein globule without the unique three-dimensional structure: experimental data for alpha-lactalbumins and general model]. (1982) (13)
A tale of two tails: The importance of unstructured termini in the aggregation pathway of β2‐microglobulin (2017) (13)
Effect of protein structure on evolution of cotranslational folding (2020) (12)
CoC: a database of universally conserved residues in protein folds (2005) (12)
Substrate inhibition imposes fitness penalty at high protein stability (2018) (12)
Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential (2021) (12)
Importance of DNA repair in tumor suppression. (2004) (12)
All-Atom Model for Stabilization of α-Helical Structure in Peptides by Hydrocarbon Staples (2009) (12)
Protein folding, evolution and design (2001) (12)
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins (2008) (12)
Semiconservative quasispecies equations for polysomic genomes: the haploid case. (2006) (12)
Random heteropolymers in layered fluids (1990) (11)
[Fluctuating state of the protein globule]. (1983) (11)
Absence of Selection for Quantum Coherence in the Fenna–Matthews–Olson Complex: A Combined Evolutionary and Excitonic Study (2017) (11)
Globular state of branched random heteropolymers (1993) (11)
Freezing of compact random heteropolymers with correlated sequence fluctuations (1998) (11)
Analytical approach to the protein design problem (1999) (10)
The emergence of scaling in sequence-based physical models of protein evolution. (2004) (10)
Sequence correlations shape protein promiscuity. (2010) (10)
Protein dynamics: From the native to the unfolded state and back again (1995) (10)
Description of atomic burials in compact globular proteins by Fermi‐Dirac probability distributions (2006) (10)
Glassy dynamics of side-chain ordering in a simple model of protein folding. (2002) (10)
Geometric and physical considerations for realistic protein models. (2005) (9)
Simulation-guided enzyme discovery: A new microbial source of cellobiose 2-epimerase. (2019) (9)
Host-parasite coevolution and optimal mutation rates for semiconservative quasispecies. (2004) (9)
Thermodynamics and kinetics of protein folding (1995) (9)
Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape. (2018) (9)
Imperfect DNA lesion repair in the semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape. (2004) (9)
The evolution dynamics of model proteins. (2004) (8)
Folding and binding: the conformational repertoire of proteins: folding, aggregation and structural recognition. (2006) (8)
The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant (2019) (8)
Exhaustive enumeration of protein conformations using experimental restraints (1995) (8)
Effect of RNA on morphology and dynamics of membraneless organelles (2021) (8)
A STUDY ON LOCAL-GLOBAL COOPERATIVITY IN PROTEIN COLLAPSE (1999) (8)
Protein folding: Think globally, (inter)act locally (1998) (8)
DISORDER IN PROTEIN STRUCTURE AND FUNCTION (1998) (7)
Stability study of icosahedral phases in diblock copolymer melt (1998) (7)
The physics of liquid-to-solid transitions in multi-domain protein condensates (2022) (7)
Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space. (2017) (7)
Frozen phases with re-entrant transition for random heteropolymers with composition specific and annealed cross-links (1997) (7)
Phase diagram analysis of random heteropolymers with composition specific and quenched cross-links (1998) (7)
Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations (2007) (7)
Proteins with selected sequences: a heteropolymeric study. (2000) (7)
A macroscopic device described by a Boltzmann-like distribution (2013) (6)
Divergent evolution of a structural proteome: phenomenological models. (2007) (6)
Phase diagram for unzipping DNA with long-range interactions. (2001) (6)
Development of antibacterial compounds that constrain evolutionary pathways to resistance (2021) (6)
Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype (2019) (6)
A native chemical chaperone in the human eye lens (2020) (6)
Fluctuation effects on microphase separation in a random copolymer Hamiltonian (1994) (6)
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes (2018) (6)
Graph's Topology and Free Energy of a Spin Model on the Graph. (2016) (6)
Freezing in polyampholytes globules: Influence of the long-range nature of the interaction (1999) (6)
Sensitivity-dependent model of protein–protein interaction networks (2006) (6)
A one-shot germinal center model under protein structural stability constraints (2013) (6)
Fold recognition with minimal gaps (2003) (5)
A Simple Model of Protein Domain Swapping in Crowded Cellular Environments. (2016) (5)
Diversity Against Adversity: How Adaptive Immune System Evolves Potent Antibodies (2011) (5)
Solvation versus freezing in a heteropolymer globule. (2003) (5)
Protein folding roller coaster, one molecule at a time (2009) (5)
Selective advantage for conservative viruses. (2004) (5)
Improvisation in evolution of genes and genomes: whose structure is it anyway? (2008) (5)
Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes (2009) (5)
Mutation rate variability as a driving force in adaptive evolution (2018) (5)
Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins (2020) (5)
Microphase separation in randomly branched polymers (1993) (5)
Modeling the kinetics of acylation of insulin using a recursive method for solving the systems of coupled differential equations. (2000) (4)
Conformational catalysis of cataract-associated aggregation in a human eye lens crystallin occurs via interface stealing (2019) (4)
Cooperativity of Protein Folding and the Random-Field Ising Model (1996) (4)
Orientational ordering in sequence-disordered liquid crystalline polymers (1999) (4)
Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition. (2008) (4)
From Knowledge‐Based Potentials to Combinatorial Lead Design in Silico (2002) (4)
In SilicoFragment-Based Generation of Drug-Like Compounds (2011) (4)
Gene Dosage Experiments in Enterobacteriaceae Using Arabinose-regulated Promoters (2014) (4)
Avoidance of protein unfolding constrains protein stability in long-term evolution. (2021) (4)
[On DNA compaction in diluted polymeric solutions]. (1981) (3)
Effects of single mutations on protein stability are Gaussian distributed (2019) (3)
Scale-Free Evolution (2006) (3)
Correction to Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants. (2018) (3)
Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations. (2011) (3)
[When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible]. (1999) (3)
Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity (2019) (3)
Evolutionary dynamics determines adaptation to inactivation of an essential gene (2019) (3)
A case of ‘mistaken identity’: structurally similar ligand inhibits Thymidylate Kinase causing reversible filamentation of E. coli (2019) (3)
Is catalytic activity of chaperones a selectable trait for the emergence of heat shock response? (2015) (3)
Disordered heteropolymers with cross-links – phase diagram and conformational transitions (1998) (3)
[A theory of heteropolymers with frozen random primary structure: properties of the globular state, coil-globule transitions and possible biophysical applications]. (1986) (3)
Liquid-liquid microphase separation leads to formation of membraneless organelles (2019) (3)
Development of antibacterial compounds that block evolutionary pathways to resistance (2020) (2)
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes (2017) (2)
Mechanical Model of Globular Transition in Polymers (2015) (2)
Gutin, Abkevich, and Shakhnovich Reply: (1998) (2)
The well-tempered protein (1999) (2)
Energy Profile of the Space of Model Protein Sequences (2001) (2)
[Theory of DNA compactization in a polymer solution]. (1981) (2)
An Exact Model of Fluctuations in Gene Expression (2004) (2)
Exotic phase transitions in disordered globular networks (2001) (2)
Conformational catalysis of cataract-associated aggregation by interacting intermediates in a human eye lens crystallin (2019) (2)
A systems-guided approach to discover the intracellular target of a novel evolution-drug lead (2021) (2)
Protein abundances and interactions coevolve to promote functional complexes while suppressing non-specific binding (2010) (2)
Overcoming the Crudeness of Energy Estimates in Protein 3 D Structure Prediction by Homologs : The When and the How (2000) (2)
Virtual Screening of Human O-GlcNAc Transferase Inhibitors (2016) (2)
Emergence of order in condensates composed of multi-valent, multi-domain proteins (2021) (1)
Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity (2021) (1)
Thermal Half-Lives of Azobenzene Derivatives: Virtual Screening Based on Intersystem Crossing Using a Machine Learning Potential (2022) (1)
Exploring the mutational robustness of nucleic acids by searching genotype neighbourhoods in sequence space (2016) (1)
Folding thermodynamics and kinetics in all-atom simulations (2000) (1)
DNA unzipping phase diagram calculated via replica theory. (2007) (1)
Different states and the associated fates of biomolecular condensates. (2022) (1)
Field theory and segmental alignment analysis for a solution of sequence disordered liquid crystalline polymers (2002) (1)
Improved fragment-based movement with LRFragLib for all-atom Ab initio protein folding (2019) (1)
Growth tradeoffs produce complex microbial communities without direct interactions (2018) (1)
Monte-Carlo Methods in Studies of Protein Folding and Evolution (2006) (1)
Semiconservative replication in the quasispecies model II: Generalization to arbitrary lesion repair probabilities (2004) (1)
SmoG: A Ligand Design Method Based on Knowledge-Based Parametrization of a Solvent Reorganization Model (1999) (1)
Enumeration with Constraints: A Possible Approach to Protein Structure Reconstruction from NMR Data (1994) (1)
The role of evolutionary selection in the dynamics of protein structure evolution (2016) (1)
Author response: Common activation mechanism of class A GPCRs (2019) (1)
Co-translational folding allows misfolding-prone proteins to circumvent deep kinetic traps (2019) (1)
Construction of Drug‐Like Compounds by Markov Chains (2013) (1)
Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype (2021) (1)
DBFOLD: An efficient algorithm for computing folding pathways of complex proteins (2020) (1)
Towards Unifying Protein Evolution Theory (2007) (1)
Of sequence and structure: Strategies of protein thermostability in evolutionary perspective (2004) (1)
Scale-Free Evolution: From Proteins to Organisms (2013) (1)
Positive and negative design in thermal adaptation of natural proteins (2006) (1)
Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity. (2021) (0)
Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates (2023) (0)
Disorder in Protein Structure and Function - Session Introduction (1999) (0)
Author response: Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak (2019) (0)
High-Throughput Disulfide Scanning of In Vivo Protein Conformations (2021) (0)
Catalysis of cataract-associated human γD crystallin aggregation via dynamic disulfide exchange (2018) (0)
E. coli DHFR complex modeled with two ligand states (2019) (0)
EMERGING BIOPHYSICAL MECHANISM AND EVOLUTION: SYNERGISTIC APPROACHES TO PREDICT EVOLUTIONARY DYNAMICS TO FIGHT DRUG RESISTANCE (2021) (0)
Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance (2023) (0)
Design of Proteins with Specified Thermal Properties (1996) (0)
Physics and Evolution of Protein‐Protein Interactions (2006) (0)
Decision letter: Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry (2019) (0)
Emergence of mutationally robust proteins in a microscopic model of evolution (2008) (0)
On-pathway multivalency of a broadly neutralizing evolution drug candidate (2021) (0)
[Solid interactions in statistical physics of biopolymers]. (1987) (0)
Kinetics of the protein folding transition (2001) (0)
Chakraborty and Shakhnovich Reply (1997) (0)
Protein folding, evolution and design : Varenna on Lake Como, Villa Monastero, 11-21 July 2000 (2001) (0)
Disulfide Exchange and Self-Catalyzed Aggregation in Cataract-Associated Human Gamma-D Crystallin (2019) (0)
Slowly replicating lytic viruses: persistence and within-host competition (2008) (0)
The Evopopbot Chip: Ultra High-throughput Evolutionary Population Bottlenecking using Drop-Based Microfluidics (2014) (0)
Catalysis of Aggregation by Interface Opening and Disulfide Exchange in Cataract-Associated Variants of Human Gamma-D Crystallin (2020) (0)
Diversity against adversity: How adaptive immunity evolves potent antibodies (2008) (0)
Development of evolution drugs - antibacterial compounds that block pathways to resistance (2020) (0)
Information and Protein Interfaces (2006) (0)
Mapping the space of photoswitchable ligands and photodruggable proteins with computational modeling (2023) (0)
Statistical Physics of Heteropolymers and Protein Folding Problem (2000) (0)
Population Genetics of Single-cell Variation in Microbial Growth (2018) (0)
Universal proteomic predictor of habitat temperature in prokaryotes (2006) (0)
Evolution: from atoms to organisms (2011) (0)
Mapping Protein Folding on Organismal Fitness One Mutation at a Time (2013) (0)
Elucidating the Structure of Aggregation-Prone Intermediate Conformations in Diverse Point Mutants of Human γD-Crystallin (2020) (0)
Repurposing of rutin for the inhibition of norovirus replication (2015) (0)
Growth tradeoffs produce complex microbial communities on a single limiting resource (2018) (0)
Emergence of the protein universe in organismal evolution (2006) (0)
Protein-Protein interaction networks: why static MpK model works and preferential attachment does not (2007) (0)
Cotranslational formation of disulfides guides folding of the SARS COV-2 receptor binding domain (2022) (0)
5 Towards Unifying Protein Evolution Theory (2007) (0)
[Fusion of heteropolymeric chains in a case in which the energy of cooperativity depends on the type of boundaries between the helical and coiled segments]. (1980) (0)
Statistical mechanics of a cross-linked polymer blend (1996) (0)
Author response: Dynamic metastable long-living droplets formed by sticker-spacer proteins (2020) (0)
Mutational robustness emerges in a microscopic model of protein evolution (2009) (0)
Domain‐swapped dimeric γ‐crystallin: the missing link in the evolution of oligomeric β‐crystallins (2022) (0)
Structural Studies of Designed Chimeric Proteins and Predictions of Mutational Effects (2021) (0)
Comment on "A Criterion that determines foldability of proteins" by D. Klimov and D. Thirumalai (PRL,v.76, p.4070 (1996)) (1996) (0)
Systematic discovery of non-native protein conformations and their molecular and cellular phenotypes (2022) (0)
Systematic conformation-to-phenotype mapping via limited deep-sequencing of proteins (2022) (0)
E. coli DHFR substrate complex with Dihydrofolate (2019) (0)
Disulfide Transfer Enables Inverse-Prion Aggregation in Mixtures of Human Gamma-D Crystallin Variants (2018) (0)
Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase (2023) (0)
Biological Sciences: Biophysics (2004) (0)
Sequence analysis Determining functional speciﬁcity from protein sequences (2005) (0)
E. coli DHFR product complex with (6S)-5,6,7,8-TETRAHYDROFOLATE (2019) (0)
Dynamic charge-density correlation function in weakly charged polyampholyte globules. (1999) (0)
311 Simple physical model for protein – protein interaction networks 365 Kinase activity in development of bone from cartilage 395 Antibody diversification via cytidine deaminase phosphorylation 472 Flavonoid regulator in axillary bud outgrowth 483 Visual Pavlovian conditioning (2005) (0)
Field Theory and Orientational Phase Ordering of Sequence Disordered LC Heteropolymers (2002) (0)
networks From The Cover : A simple physical model for scaling in protein-protein interaction (2009) (0)
Carbonic Anhydrase II Complexed With N-[2-(1H-Indol-5-yl)-butyl]-4-sulfamoyl-benzamide (2001) (0)
Emergence of clonal selection and affinity maturation in an ab initio microscopic model of immunity (2007) (0)
E. coli DHFR ternary complex with NADP and dihydrofolate (2019) (0)
Empowering systems-guided drug target discovery with metabolic and structural analysis (2022) (0)
Effect of dynamical cross-links on the incoherent scattering of a single macromolecule (2004) (0)
Climbing the scales ladder in Biology one mutation at a time (2014) (0)
Universal activation mechanism of class A GPCRs (2019) (0)
Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microﬂuidics (2015) (0)
CHAPTER 10 Scale-Free Evolution : From Proteins to Organisms (2005) (0)
The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: insights from molecular simulations of D76N mutant (2018) (0)
Theory of Kinetic Partitioning in Protein Folding (With Application to Prions) (1996) (0)
The Behavior of Random Heteropolymers in Disordered Media: Replica Symmetry Breaking and ``Folded'' Phases (1996) (0)
Thermodynamics of the Hairpin Ribozyme from All-Atom Simulations (2006) (0)
Concentration dependent model of protein-protein interaction networks (2006) (0)
Carbonic Anhydrase II Complexed With (R)-N-(3-Indol-1-yl-2-methyl-propyl)-4-sulfamoyl-benzamide (2001) (0)
Faculty Opinions recommendation of On the relationship between protein stability and folding kinetics: a comparative study of the N-terminal domains of RNase HI, E. coli and Bacillus stearothermophilus L9. (2001) (0)
Phase Transformations and Orientational Ordering in Chemically Disordered Polymers — a Modern Primer (2004) (0)
Evolutionary Dynamics of a Lattice Dimer: a Toy Model for Stability vs. Affinity Trade-offs in Proteins (2023) (0)
Di ff erential Enzyme Flexibility Probed Using Solid-State Nanopores (2018) (0)
Reply to the comment by C.Camacho on PRL, v.77, p.5433 (1997) (0)
Population genetics with selection on multiple phases of microbial growth (2017) (0)
Imperfect DNA Repair and the Error Catastrophe (2004) (0)
Thermodynamics and kinetic analysis of the SH3 fold (2002) (0)
Adaptation to mutational inactivation of an essential E. coli gene converges to an accessible suboptimal fitness peak (2019) (0)
Author response: Development of antibacterial compounds that constrain evolutionary pathways to resistance (2021) (0)
Adaptation through stochastic switching into transient mutators in finite asexual populations (2009) (0)
Biophysical Walks on Fitness Landscapes (2018) (0)
Can a Protein's Evolutionary Fate be Predicted from its Structure? (2014) (0)
Accurate protein-folding transition-path statistics from a simple free-energy landscape (2018) (0)
Systematic Conformation‐to‐Phenotype Mapping via Limited Protein Sequencing (2022) (0)
Understanding Biological Fitness From First Principles (2011) (0)
Proteins with Selected Sequences Fold into Unique Native Conformation [Phys. Rev. Lett. 72, 3907 (1994)] (1995) (0)

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