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List of works by Eugene I. Shakhnovich

A Simple Model of Protein Domain Swapping in Crowded Cellular Environments

scientific article published on June 2016

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor ⬇️

scientific article published on December 27, 2012

A biophysical protein folding model accounts for most mutational fitness effects in viruses ⬇️

scientific article published on May 24, 2011

A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds

scientific article

A knowledge-based move set for protein folding

scientific article published in February 2007

A native chemical chaperone in the human eye lens

scientific article published in 2022

A new approach to the design of stable proteins

scientific article

A one-shot germinal center model under protein structural stability constraints ⬇️

scientific article published on March 15, 2013

A protein engineering analysis of the transition state for protein folding: simulation in the lattice model ⬇️

scientific article published on January 1, 1998

A simple physical model for scaling in protein-protein interaction networks

scientific article

A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior

scientific article

A structure-based method for derivation of all-atom potentials for protein folding

scientific article

A structure-centric view of protein evolution, design, and adaptation.

scientific article

A test of lattice protein folding algorithms

scientific article

A theory of heteropolymers with frozen random primary structure: properties of the globular state, coil-globule transitions and possible biophysical applications

scientific article published in November 1986

Absence of Selection for Quantum Coherence in the Fenna-Matthews-Olson Complex: A Combined Evolutionary and Excitonic Study

scientific article published on 30 August 2017

Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape.

scientific article published on 22 August 2018

Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak

scientific article published on 01 October 2019

All-atom model for stabilization of alpha-helical structure in peptides by hydrocarbon staples

scientific article

Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases

scholarly article

An Internal Disulfide Locks a Misfolded Aggregation-prone Intermediate in Cataract-linked Mutants of Human γD-Crystallin

scientific article published on 14 July 2016

Analysis of knowledge-based protein-ligand potentials using a self-consistent method

scientific article published on April 2000

Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations

scientific article published on 22 August 2013

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

scientific article

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations

scientific article published on 31 October 2016

Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations

scientific article published on 7 November 2013

Combinatorial computational method gives new picomolar ligands for a known enzyme

scientific article

Commitment and nucleation in the protein G transition state

scientific article published in February 2004

Common activation mechanism of class A GPCRs

scientific article published on 19 December 2019

Common motifs and topological effects in the protein folding transition state

scientific article

Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score

scientific article published in November 2000

Computer simulations of prebiotic evolution ⬇️

scientific article published on January 1, 1997

Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size

scientific article published on 5 August 2008

Contribution of selection for protein folding stability in shaping the patterns of polymorphisms in coding regions

scientific article published on 11 October 2013

DNA unzipping phase diagram calculated via replica theory

scientific article published on 28 May 2009

De novodesign: balancing novelty and confined chemical space ⬇️

scientific article published on June 30, 2010

Determining functional specificity from protein sequences

scientific article published on 29 March 2005

Different circular permutations produced different folding nuclei in proteins: a computational study

scientific article

Direct molecular dynamics observation of protein folding transition state ensemble

scientific article

Discrete molecular dynamics studies of the folding of a protein-like model

scientific article published in January 1998

Divergent evolution of a structural proteome: phenomenological models

scientific article published on 27 October 2006

Domains in folding of model proteins

scientific article published on June 1995

Dynamic disulfide exchange in a crystallin protein in the human eye lens promotes cataract-associated aggregation

scientific article published in Journal of Biological Chemistry

Dynamic metastable long-living droplets formed by sticker-spacer proteins

scientific article published on 02 June 2020

Dynamics of heteropolymers in dilute solution: Effective equation of motion and relaxation spectrum

scientific article published in November 1996

ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations

scientific article

Effect of RNA on Morphology and Dynamics of Membraneless Organelles

scientific article published on 10 May 2021

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

scientific article published in June 2017

Emergence of species in evolutionary "simulated annealing".

scholarly article

Energetics of protein-DNA interactions

scientific article published on 26 January 2007

Engineering of stable and fast-folding sequences of model proteins

scientific article

Entropic stabilization of proteins and its proteomic consequences

scientific article

Equilibrium Distribution of Mutators in the Single Fitness Peak Model ⬇️

scientific article published on September 26, 2003

Evidence of evolutionary selection for cotranslational folding

scientific article

Evolution of specificity in protein-protein interactions

scientific article

Evolution on the Biophysical Fitness Landscape of an RNA Virus

scholarly article by Assaf Rotem published in October 2018

Evolution-like selection of fast-folding model proteins

scientific article

Excluded volume in protein side-chain packing

scientific article published in August 2001

Expanding protein universe and its origin from the biological Big Bang

scientific article

Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space

scientific article published on 3 January 2017

Exploring the mutational robustness of nucleic acids by searching genotype neighbourhoods in sequence space

FOG: Fragment Optimized Growth algorithm for the de novo generation of molecules occupying druglike chemical space

scientific article

Fluctuating state of the protein globule

scientific article

Folding Kinetics of Villin 14T, a Protein Domain with a Central β-Sheet and Two Hydrophobic Cores ⬇️

scientific article published on October 13, 1998

From knowledge-based potentials to combinatorial lead design in silico

scientific article

Functional fingerprints of folds: evidence for correlated structure-function evolution

scientific article published on February 2003

Gene Dosage Experiments in Enterobacteriaceae Using Arabinose-regulated Promoters

scientific article published in July 2014

Geometric and physical considerations for realistic protein models.

scientific article

Graph's Topology and Free Energy of a Spin Model on the Graph ⬇️

scientific article published on 24 February 2017

Growth tradeoffs produce complex microbial communities on a single limiting resource

scientific article published in Nature Communications

High-resolution protein folding with a transferable potential

scholarly article

Highly abundant proteins favor more stable 3D structures in yeast

scientific article published in February 2013

Hiking in the energy landscape in sequence space: a bumpy road to good folders

scientific article published in May 2000

How the first biopolymers could have evolved

scientific article

How to derive a protein folding potential? A new approach to an old problem

scientific article

Identification of the minimal protein-folding nucleus through loop-entropy perturbations

scholarly article

Identifying importance of amino acids for protein folding from crystal structures

scientific article published in January 2003

Identifying the protein folding nucleus using molecular dynamics.

scientific article

Impact of local and non-local interactions on thermodynamics and kinetics of protein folding

scientific article

Imperfect DNA lesion repair in the semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape

scientific article published on 30 December 2004

Imprint of evolution on protein structures.

scientific article

Improvisation in evolution of genes and genomes: whose structure is it anyway?

scientific article

Influence of point mutations on protein structure: probability of a neutral mutation

scientific article

Influenza A H1N1 pandemic strain evolution--divergence and the potential for antigenic drift variants.

scientific article

Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response

scientific article

Is catalytic activity of chaperones a selectable trait for the emergence of heat shock response?

scientific article published on January 2015

Is there an en route folding intermediate for cold shock proteins? ⬇️

scientific article published on March 29, 2012

Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics

scientific article published on 13 May 2015

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

scientific article

Lessons from the design of a novel atomic potential for protein folding

scientific article

Lethal mutagenesis in viruses and bacteria

scientific article published on 20 July 2009

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics

scientific article

Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding

scientific article

Mode-coupling theory for heteropolymers

scientific article published on 20 March 2001

Modeling protein folding: the beauty and power of simplicity

scientific article

Modeling the kinetics of acylation of insulin using a recursive method for solving the systems of coupled differential equations

scientific article published on February 2000

Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism

scientific article

Multi-Scale Sequence Correlations Increase Proteome Structural Disorder and Promiscuity ⬇️

scientific article published on April 2, 2011

Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation

scientific article

Native atom types for knowledge-based potentials: application to binding energy prediction

scientific article published in August 2004

Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins

scientific article published in February 2008

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

scientific article

Non‐native interactions play an effective role in protein folding dynamics ⬇️

scientific article published on November 1, 2010

Nucleation and the transition state of the SH3 domain

scientific article

On the origin and highly likely completeness of single-domain protein structures.

scientific article

OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands

scientific article published on 10 September 2015

Optimality of mutation and selection in germinal centers

scientific article

Optimization of lag phase shapes the evolution of a bacterial enzyme.

scientific article

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

scientific article

Phase diagram for unzipping DNA with long-range interactions

scientific article published on 19 September 2002

Physics and evolution of thermophilic adaptation

scientific article

Positive and negative design in stability and thermal adaptation of natural proteins

scientific article

Positively selected sites in cetacean myoglobins contribute to protein stability

scientific article

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

scientific article

Prokaryotic phylogenies inferred from protein structural domains

scientific article published on March 2005

Protein Evolution within a Structural Space ⬇️

scientific article published on November 1, 2003

Protein and DNA sequence determinants of thermophilic adaptation

scientific article

Protein biophysics explains why highly abundant proteins evolve slowly

scientific article

Protein design: a perspective from simple tractable models ⬇️

scientific article published on January 1, 1998

Protein folding roller coaster, one molecule at a time

scientific article published on 15 July 2009

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

scientific article

Protein folding: think globally, (inter)act locally

scientific article

Protein globule without the unique three-dimensional structure: experimental data for alpha-lactalbumins and general model

scientific article published on November 1982

Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness

scientific article published on 6 December 2012

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

scholarly article

Protein structure and evolutionary history determine sequence space topology

scientific article

Protein structure prediction by threading. why it works and why it does not 1 1Edited by F. Cohen ⬇️

scientific article published on October 23, 1998

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

scientific article

Proteomic traces of speciation

scientific article published in February 2004

Pseudodihedrals: simplified protein backbone representation with knowledge-based energy

scientific article published on September 1994

Quantifying fitness distributions and phenotypic relationships in recombinant yeast populations

scholarly article

Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants

scientific article published on 19 May 2017

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations

scientific article

Repurposing of rutin for the inhibition of norovirus replication

scientific article published on 26 June 2015

Robust protein protein interactions in crowded cellular environments

scholarly article

Robustness of atomistic Gō models in predicting native-like folding intermediates ⬇️

scientific article published on August 28, 2012

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

scientific article published on 16 October 2008

SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions

scientific article published in June 2002

Searching the Sequence Space for Potent Aptamers Using SELEX in Silico

scientific article published on 5 November 2015

Selective advantage for conservative viruses

scientific article published on 8 March 2005

Semiconservative quasispecies equations for polysomic genomes: the haploid case

scientific article published on 9 March 2006

Sensitivity-dependent model of protein-protein interaction networks

scientific article published on 29 September 2008

Side-chain dynamics and protein folding.

scientific article

Simulation, experiment, and evolution: understanding nucleation in protein S6 folding

scholarly article

Simulations of chaperone-assisted folding

scientific article published in January 1996

Slowly replicating lytic viruses: pseudolysogenic persistence and within-host competition

scientific article

Solid interactions in statistical physics of biopolymers

scientific article published in November 1987

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations

scientific article published on 12 March 2012

Solution of the quasispecies model for an arbitrary gene network

scientific article published on 11 August 2004

Specific nucleus as the transition state for protein folding: evidence from the lattice model

scientific article published in August 1994

Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics

scientific article published on 3 January 2018

Statistical significance of protein structure prediction by threading.

scientific article

Statistically enhanced promiscuity of structurally correlated patterns

scientific article published in February 2008

Structural and energetic determinants of co-translational folding

scientific article published in June 2013

Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential

scientific article published in July 2004

Structure-Based Prediction of Protein-Folding Transition Paths ⬇️

scientific article

Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity

scientific article published in 2021

Systems-level evidence of transcriptional co-regulation of yeast protein complexes

scientific article published in February 2009

The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution

scientific article

The emergence of scaling in sequence-based physical models of protein evolution

scientific article

The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation

scientific article

The ensemble folding kinetics of the FBP28 WW domain revealed by an all‐atom Monte Carlo simulation in a knowledge‐based potential ⬇️

scientific article published on March 1, 2011

The folding mechanics of a knotted protein

scientific article

The influence of selection for protein stability on dN/dS estimations

scientific article

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential.

scientific article

Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition

scientific article

Theory of kinetic partitioning in protein folding with possible applications to prions ⬇️

scientific article published on June 1, 1998

Thermal adaptation of viruses and bacteria

scientific article

Thermal stabilization of dihydrofolate reductase using monte carlo unfolding simulations and its functional consequences

scientific article published on 23 April 2015

Thermodynamics and Kinetics of the Hairpin Ribozyme from Atomistic Folding/Unfolding Simulations ⬇️

scientific article published on June 30, 2011

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics

scientific article

Topological determinants of protein folding

scientific article

Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions ⬇️

scientific article published on February 22, 2011

Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection

scientific article published on 01 February 2018

Transient protein-protein interactions perturb E. coli metabolome and cause gene dosage toxicity.

scientific article published on 10 December 2016

Understanding ensemble protein folding at atomic detail

scholarly article

Understanding protein evolution: from protein physics to Darwinian selection

scientific article published on January 2008

Universality and diversity of folding mechanics for three-helix bundle proteins

scholarly article

Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

scientific article

Using protein design for homology detection and active site searches

scientific article

Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins

scientific article published on 16 November 2020

What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis

scientific article published in July 2000

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