List of works - Nikolay V. Dokholyan

Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function

scholarly article

Eris: an automated estimator of protein stability

scientific article published in June 2007

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

scientific article published in January 1998

Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

scientific article

Ab initio folding of proteins with all-atom discrete molecular dynamics

scientific article published on July 2008

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

scientific article published on 2 May 2008

Small-world view of the amino acids that play a key role in protein folding

scientific article published on 25 June 2002

Automated minimization of steric clashes in protein structures

scientific article

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

scientific article published on 23 February 2012

Emergence of protein fold families through rational design

scientific article

Engineered allosteric activation of kinases in living cells

scientific article

Mechanism for the alpha-helix to beta-hairpin transition

scientific article

iFoldRNA: three-dimensional RNA structure prediction and folding

scientific article

Modeling backbone flexibility improves protein stability estimation

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

Molecular dynamics simulation of amyloid beta dimer formation

scientific article published on October 2004

Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

article by Nikolay V. Dokholyan & Eugene I. Shakhnovich published September 2001 in Journal of Molecular Biology

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

scientific article

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

scientific article published on 16 April 2015

Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating

scientific article

Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis

scientific article published on 19 March 2009

The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis

scientific article

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization

scientific article

Identifying the protein folding nucleus using molecular dynamics

scientific article

MedusaScore: an accurate force field-based scoring function for virtual drug screening

scientific article published on 02 August 2008

Direct molecular dynamics observation of protein folding transition state ensemble

scientific article

Outcome of a workshop on applications of protein models in biomedical research

scientific article (publication date: 13 February 2009)

The complex molecular biology of amyotrophic lateral sclerosis (ALS)

scientific article

Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein

scientific article published on 26 October 2012

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

scientific article

Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences

scientific article

Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR

scientific article published on 16 June 2010

Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP.

scientific article published on 16 December 2010

On the significance of an RNA tertiary structure prediction

scientific article

Multiscale modeling of nucleosome dynamics

scientific article published on December 2006

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics

scientific article published in February 2009

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

scholarly article

Single-molecule correlated chemical probing of RNA.

scientific article

Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR.

scientific article

Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants

scholarly article

Computational design of a PAK1 binding protein

scientific article

Engineering extrinsic disorder to control protein activity in living cells

scientific article

Fast complementation of split fluorescent protein triggered by DNA hybridization

scholarly article

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

scientific article

Topological Determinants of Protein Domain Swapping

article published in 2006

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

scientific article

Rational design of a ligand-controlled protein conformational switch

scientific article published on 8 April 2013

Three-dimensional RNA structure refinement by hydroxyl radical probing

scientific article

List of works by Nikolay V. Dokholyan

Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function

Eris: an automated estimator of protein stability

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

Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

Ab initio folding of proteins with all-atom discrete molecular dynamics

Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

Small-world view of the amino acids that play a key role in protein folding

Automated minimization of steric clashes in protein structures

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

Emergence of protein fold families through rational design

Engineered allosteric activation of kinases in living cells

Mechanism for the alpha-helix to beta-hairpin transition

iFoldRNA: three-dimensional RNA structure prediction and folding

Modeling backbone flexibility improves protein stability estimation

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

Molecular dynamics simulation of amyloid beta dimer formation

Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

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

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating

Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis

The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization

Identifying the protein folding nucleus using molecular dynamics

MedusaScore: an accurate force field-based scoring function for virtual drug screening

Direct molecular dynamics observation of protein folding transition state ensemble

Outcome of a workshop on applications of protein models in biomedical research

The complex molecular biology of amyotrophic lateral sclerosis (ALS)

Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences

Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR

Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP.

On the significance of an RNA tertiary structure prediction

Multiscale modeling of nucleosome dynamics

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

Single-molecule correlated chemical probing of RNA.

Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR.

Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants

Computational design of a PAK1 binding protein

Engineering extrinsic disorder to control protein activity in living cells

Fast complementation of split fluorescent protein triggered by DNA hybridization

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Topological Determinants of Protein Domain Swapping

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

Rational design of a ligand-controlled protein conformational switch

Three-dimensional RNA structure refinement by hydroxyl radical probing