List of works - Eugene I. Shakhnovich

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

scientific article published in August 1994

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

scientific article

Engineering of stable and fast-folding sequences of model proteins

scientific article

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

scientific article published in January 1998

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

scientific article

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

scientific article

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

scholarly article

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

scientific article published on 01 October 1989

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

scientific article

Protein and DNA sequence determinants of thermophilic adaptation

scientific article published on 30 November 2006

A new approach to the design of stable proteins

scientific article

Physics and evolution of thermophilic adaptation

scientific article

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

scientific article

Expanding protein universe and its origin from the biological Big Bang

scientific article

Topological determinants of protein folding

scientific article

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

scientific article published on May 24, 2011

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

scientific article

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

scientific article

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

scientific article

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

scientific article

A test of lattice protein folding algorithms

scientific article

Evolution-like selection of fast-folding model proteins

scientific article

Identifying the protein folding nucleus using molecular dynamics

scientific article

Direct molecular dynamics observation of protein folding transition state ensemble

scientific article

The folding mechanics of a knotted protein

scientific article

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

scientific article published on 6 December 2012

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

scientific article

Protein design: a perspective from simple tractable models

scientific article published on January 1, 1998

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

scientific article published on February 22, 2011

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

scientific article published on 5 August 2008

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

scholarly article

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

scientific article published in July 2000

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

scientific article

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations

scientific article published on 12 March 2012

Protein biophysics explains why highly abundant proteins evolve slowly

scientific article

Understanding protein evolution: from protein physics to Darwinian selection

scientific article published on January 2008

Robust protein protein interactions in crowded cellular environments

scholarly article

Protein structure and evolutionary history determine sequence space topology

scientific article

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

scientific article published in June 2002

Energetics of protein-DNA interactions

scientific article published on 26 January 2007

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

scientific article

Entropic stabilization of proteins and its proteomic consequences

scientific article

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

scientific article

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

scientific article published in July 2007

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

scientific article

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

scholarly article

Understanding ensemble protein folding at atomic detail

scholarly article

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

scientific article published on June 19, 2014

Lethal mutagenesis in viruses and bacteria

scientific article published on 20 July 2009

Commitment and nucleation in the protein G transition state

scientific article published in February 2004

List of works by Eugene I. Shakhnovich

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

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

Engineering of stable and fast-folding sequences of model proteins

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

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

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

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

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

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

Protein and DNA sequence determinants of thermophilic adaptation

A new approach to the design of stable proteins

Physics and evolution of thermophilic adaptation

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

Expanding protein universe and its origin from the biological Big Bang

Topological determinants of protein folding

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

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

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

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

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

A test of lattice protein folding algorithms

Evolution-like selection of fast-folding model proteins

Identifying the protein folding nucleus using molecular dynamics

Direct molecular dynamics observation of protein folding transition state ensemble

The folding mechanics of a knotted protein

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

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

Protein design: a perspective from simple tractable models

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

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

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

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

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

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations

Protein biophysics explains why highly abundant proteins evolve slowly

Understanding protein evolution: from protein physics to Darwinian selection

Robust protein protein interactions in crowded cellular environments

Protein structure and evolutionary history determine sequence space topology

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

Energetics of protein-DNA interactions

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

Entropic stabilization of proteins and its proteomic consequences

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

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

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

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

Understanding ensemble protein folding at atomic detail

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

Lethal mutagenesis in viruses and bacteria

Commitment and nucleation in the protein G transition state