List of works by Nikolay V. Dokholyan

A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation

scientific article published on 17 September 2016

A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization

scientific article published on 31 December 2016

A central core disease mutation in the Ca2+-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation

scientific article published on 05 June 2019

A didactic model of macromolecular crowding effects on protein folding

scientific article

A folding pathway-dependent score to recognize membrane proteins

scientific article

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase

scientific article published on 12 February 2016

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

scientific article

A physical model reveals the mechanochemistry responsible for dynein's processive motion

scientific article

A single disulfide bond differentiates aggregation pathways of beta2-microglobulin.

scientific article published on 7 October 2005

A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1)

scientific article

A structural model reveals energy transduction in dynein

scholarly article

ASR490, a Small Molecule, Overrides Aberrant Expression of Notch1 in colorectal cancer

scientific article published on 21 October 2020

ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions

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

scientific article published on 2 May 2008

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

scientific article published on July 2008

Active nuclear receptors exhibit highly correlated AF-2 domain motions

scientific article

Adaptation‐Proof SARS‐CoV‐2 Vaccine Design

scientific article published in 2022

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

scientific article

Allostery in Its Many Disguises: From Theory to Applications

scientific article published on 07 February 2019

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

scientific article published on 27 October 2015

Application of Quantum Tensor Networks for Protein Classification

scientific article published on 10 June 2024

Applications of Discrete Molecular Dynamics in biology and medicine

scientific article published on 27 November 2015

Approaches for probing the sequence space of substrates recognized by molecular chaperones

scientific article

Automated minimization of steric clashes in protein structures

scientific article

BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics.

scientific article

COMT gene locus: new functional variants

scientific article published on 23 July 2015

Can contact potentials reliably predict stability of proteins?

scientific article published in March 2004

Channel Gating Dependence on Pore Lining Helix Glycine Residues in Skeletal Muscle Ryanodine Receptor

scientific article published on 21 May 2015

Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening

scientific article published on 14 December 2011

Clustering of identical oligomers in coding and noncoding DNA sequences

scientific article published in August 1999

Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets

scientific article

Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins

scientific article

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

scholarly article

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.

scientific article

Computational Evaluation of Protein Stability Change upon Mutations ⬇️

scientific article published on January 1, 2010

Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities.

scientific article

Computational Protein Design Through Grafting and Stabilization

scientific article

Computational approaches to understanding protein aggregation in neurodegeneration

scientific article published on 11 March 2014

Computational design of a PAK1 binding protein

scientific article

Computational design of chemogenetic and optogenetic split proteins

scientific article published in Nature Communications

Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models

scientific article

Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR.

scientific article published on 26 March 2008

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

scientific article published on 27 March 2019

Controlling Allosteric Networks in Proteins

scientific article published on 19 February 2016

Correction to Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain

scholarly article published in Biochemistry

Correction: Emergence of Protein Fold Families through Rational Design.

scientific article published on 27 October 2006

Correction: Thermal Unfolding Pathway of PHD2 Catalytic Domain in Three Different PHD2 Species: Computational Approaches.

scientific article published on 22 April 2013

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

scientific article published on 26 October 2012

Corrigendum to “ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions” [Biochim. Biophys. Acta 1808 (2011) 2954–2964]

scholarly article published in BBA - Biomembranes

Corrigendum: Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

scientific article published on 28 April 2017

Corrigendum: Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

scientific article published on 17 February 2017

Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive

scientific article

DNA sequence mediates nucleosome structure and stability

scientific article

Deciphering protein dynamics from NMR data using explicit structure sampling and selection

scientific article

Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent

scientific article published on 21 November 2019

Differences in Conformation and Conformational Dynamics Between Cisplatin and Oxaliplatin DNA Adducts

article published in 2009

Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers

scientific article published on 5 October 2015

Differential Regulation of 6- and 7-Transmembrane Helix Variants of μ-Opioid Receptor in Response to Morphine Stimulation

scientific article published on 10 November 2015

Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding

scientific article

Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion

scientific article published in Journal of Biological Chemistry

Direct identification of base-paired RNA nucleotides by correlated chemical probing

scientific article published on November 2016

Direct molecular dynamics observation of protein folding transition state ensemble

scientific article

Discrete molecular dynamics

article

Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins

scientific article

Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets

scientific article

Discrete molecular dynamics simulations of peptide aggregation

scientific article published on 29 April 2004

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

scientific article published in January 1998

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

scientific article

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

scientific article

Distribution of shortest paths in percolation

scholarly article

Distributions of dimeric tandem repeats in non-coding and coding DNA sequences

scientific article published in February 2000

Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise

scientific article

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications

scientific article

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

scholarly article

Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability

scientific article published on March 2013

Emergence of protein fold families through rational design

scientific article

Energetic and structural basis for activation of the epithelial sodium channel by matriptase

scientific article

Engineered allosteric activation of kinases in living cells

scientific article

Engineering Pak1 Allosteric Switches

scientific article published on 3 April 2017

Engineering extrinsic disorder to control protein activity in living cells

scientific article

Engineering proteins for allosteric control by light or ligands

scientific article published on 10 May 2019

Eris: an automated estimator of protein stability.

scientific article published in June 2007

Expanding protein universe and its origin from the biological Big Bang

scientific article

FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis.

scientific article published in December 2006

Faculty of 1000 evaluation for Alzheimer's - Looking beyond plaques

Faculty of 1000 evaluation for An over-oxidized form of superoxide dismutase found in sporadic amyotrophic lateral sclerosis with bulbar onset shares a toxic mechanism with mutant SOD1

article

Faculty of 1000 evaluation for Aspartate 112 is the selectivity filter of the human voltage-gated proton channel

Faculty of 1000 evaluation for Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Faculty of 1000 evaluation for Dynamics and memory of heterochromatin in living cells

Faculty of 1000 evaluation for Early Steps in Oxidation-Induced SOD1 Misfolding: Implications for Non-Amyloid Protein Aggregation in Familial ALS

Faculty of 1000 evaluation for Generation of functional human pancreatic β cells in vitro

Faculty of 1000 evaluation for Genetic selection designed to stabilize proteins uncovers a chaperone called Spy

Faculty of 1000 evaluation for Genetic switchboard for synthetic biology applications

scholarly article published 1 May 2012

Faculty of 1000 evaluation for Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype

Faculty of 1000 evaluation for Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells

Faculty of 1000 evaluation for Kynurenine 3-monooxygenase inhibition in blood ameliorates neurodegeneration

Faculty of 1000 evaluation for Macrophage Migration Inhibitory Factor as a Chaperone Inhibiting Accumulation of Misfolded SOD1

Faculty of 1000 evaluation for Mapping intact protein isoforms in discovery mode using top-down proteomics

Faculty of 1000 evaluation for Monitoring spatiotemporal biogenesis of macromolecular assemblies by pulse-chase epitope labeling

scholarly article published 8 October 2012

Faculty of 1000 evaluation for Pathological α-synuclein transmission initiates Parkinson-like neurodegeneration in nontransgenic mice

scholarly article published 21 August 2013

Faculty of 1000 evaluation for Probing allostery through DNA

Faculty of 1000 evaluation for Protein interface conservation across structure space

Faculty of 1000 evaluation for Selective protein synthesis by ribosomes with a drug-obstructed exit tunnel

Faculty of 1000 evaluation for Small-molecule conversion of toxic oligomers to nontoxic β-sheet-rich amyloid fibrils

article

Faculty of 1000 evaluation for Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T

Faculty of 1000 evaluation for Structure of a nanobody-stabilized active state of the beta(2) adrenoceptor

Faculty of 1000 evaluation for Structure of an intermediate state in protein folding and aggregation

Faculty of 1000 evaluation for The crystal structure of a voltage-gated sodium channel

Faculty of 1000 evaluation for Three-dimensional reconstruction of protein networks provides insight into human genetic disease

Faculty of 1000 evaluation for alpha-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation

Fast complementation of split fluorescent protein triggered by DNA hybridization

scholarly article

Fast screening of protein surfaces using geometric invariant fingerprints.

scientific article

Fidelity of the protein structure reconstruction from inter-residue proximity constraints.

scientific article

Fingerprint-based structure retrieval using electron density

scientific article published on 3 January 2011

Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links

scientific article

Flow between two sites on a percolation cluster

scientific article published on 01 December 2000

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

scientific article

Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis

scientific article published in November 2003

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

scientific article published on February 2003

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase

scientific article

G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to cytosolic and luminal Ca2.

scientific article published on 18 December 2017

Gaia: automated quality assessment of protein structure models

scientific article

Gain-of-Function Mutation W493R in the Epithelial Sodium Channel Allosterically Reconfigures Intersubunit Coupling

scientific article published on 14 December 2015

Glassy behavior of a homopolymer from molecular dynamics simulations

article

Glutathionylation at Cys-111 induces dissociation of wild type and FALS mutant SOD1 dimers

scientific article published on 18 July 2011

Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks

scientific article published on 14 October 2020

Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

scientific article (publication date: 15 November 2016)

Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles

scientific article published on 5 June 2012

High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers

article

Highly covarying residues have a functional role in antibody constant domains

scientific article published on 27 February 2013

Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism

Hybrid dynamics simulation engine for metalloproteins

scientific article

Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers

scientific article

Identification of a Vitamin-D Receptor Antagonist, MeTC7, which Inhibits the Growth of Xenograft and Transgenic Tumors <i>In Vivo</i>

scientific article published on 11 April 2022

Identification of a consensus motif in substrates bound by a Type I Hsp40.

scholarly article

Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties

scientific article

Identification of novel integrin binding partners for calcium and integrin binding protein 1 (CIB1): structural and thermodynamic basis of CIB1 promiscuity

scientific 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

Imprint of evolution on protein structures.

scientific article

Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark

scientific article

Insights into Allosteric Control of Vinculin Function from Its Large Scale Conformational Dynamics

scientific article published in Journal of Biological Chemistry

Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes

scientific article published on 30 May 2007

Inter-Active Site Communication Mediated by the Dimer Interface β-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase

scientific article published on 18 July 2019

Interaction with the 5D3 monoclonal antibody is regulated by intramolecular rearrangements but not by covalent dimer formation of the human ABCG2 multidrug transporter

scientific article published on 21 July 2008

Intra- and inter-subunit disulfide bond formation is nonessential in adeno-associated viral capsids

scientific article

Intrinsic disorder mediates cooperative signal transduction in STIM1.

scientific article published on 17 March 2014

Ion-pulling simulations provide insights into the mechanisms of channel opening of the skeletal muscle ryanodine receptor

scientific article published on 05 June 2017

Isoform divergence of the filamin family of proteins

scientific article published on 5 October 2009

Kinetic models for the coordinated stepping of cytoplasmic dynein

scientific article published in January 2009

Knowledge-based design of a biosensor to quantify localized ERK activation in living cells

scientific article

Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis

article published in the Proceedings of the National Academy of Sciences of the United States of America

Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator

scientific article published on 14 June 2018

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

scientific article published on 16 December 2010

Light-cleavable rapamycin dimer as an optical trigger for protein dimerization.

scientific article published in April 2015

Limits in accuracy and a strategy of RNA structure prediction using experimental information.

scientific article published in June 2019

Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates

scientific article published on 21 December 2011

MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression

scientific article published on 03 April 2019

Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity

scientific article

Mapping allosteric communications within individual proteins

scientific article published on 31 July 2020

Mapping allosteric linkage to channel gating of extracellular domains in the human epithelial sodium channel

scientific article published on 22 January 2018

Mechanism for the alpha-helix to beta-hairpin transition

scientific article

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints

scientific article published on 17 April 2019

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

scientific article published on 02 August 2008

Metric to distinguish closely related domain families using sequence information

scientific article published on 3 December 2012

Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics

Modeling backbone flexibility improves protein stability estimation.

scientific article

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

scientific article published on 19 March 2009

Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue

scientific article

Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics

scientific article published on 23 August 2007

Molecular dynamics simulation of amyloid beta dimer formation

scientific article published on October 2004

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

scientific article

Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins

scientific article published on 20 May 2019

Molecular mechanisms of polypeptide aggregation in human diseases

scientific article published on December 2007

Molecular modeling tools and approaches for CFTR and cystic fibrosis

scientific article

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

scientific article

Multiple folding pathways of the SH3 domain

scientific article

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

scientific article

Multiscale approaches for studying energy transduction in dynein

scientific article

Multiscale modeling of nucleosome dynamics

scientific article published on December 2006

N-terminal strands of filamin Ig domains act as a conformational switch under biological forces

scientific article

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

scientific article published in February 2009

Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm

scientific article published on 23 May 2008

New Insights into FAK Signaling and Localization Based on Detection of a FAT Domain Folding Intermediate

New Models for Regulation of Vinculin by Actin and Phospholipids

New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling

scientific article published on 3 December 2012

Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX

scientific article

Non-native soluble oligomers of Cu/Zn superoxide dismutase (SOD1) contain a conformational epitope linked to cytotoxicity in amyotrophic lateral sclerosis (ALS). ⬇️

scientific article published on 02 April 2014

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

scientific article

On the significance of an RNA tertiary structure prediction

scientific article

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

scientific article (publication date: 13 February 2009)

Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases

scientific article published on 20 April 2016

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

scholarly article

Physical microscopic model of proteins under force

scientific article published on 15 March 2012

Physicochemical code for quinary protein interactions in Escherichia coli

scientific article

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

scientific article

Pore dynamics and conductance of RyR1 transmembrane domain

scientific article

Possible Mechanism for Cold Denaturation of Proteins at High Pressure

scientific article published in Physical Review Letters

Postbreakthrough behavior in flow through porous media

scholarly article

Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

scientific article

Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches

scientific article

Predicting oil recovery using percolation

scholarly article

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene

scientific article published on 26 July 2017

Prefusion spike protein stabilization through computational mutagenesis ⬇️

scientific article published on 24 November 2020

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling

scientific article published on 14 January 2013

Probing protein aggregation using discrete molecular dynamics

scientific article (publication date: May 2008)

Protein Destabilization as a Common Factor in Diverse Inherited Disorders.

scientific article

Protein Evolution within a Structural Space ⬇️

scientific article published on November 1, 2003

Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family

scientific article

Protein folding: Over half a century lasting quest: Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al.

scientific article

Protein folding: then and now

scientific article

RNA tertiary structure analysis by 2'-hydroxyl molecular interference

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

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

scientific article

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

scientific article published on 05 May 2020

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

scientific article published on 23 February 2012

RNA–DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells

scientific article published on 01 February 2019

Rapid flexible docking using a stochastic rotamer library of ligands

scientific article

Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator.

scientific article

Rational design and implementation of a chemically inducible heterotrimerization system

scientific article published on 03 August 2020

Rational design of a ligand-controlled protein conformational switch

scientific article published on 8 April 2013

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

article

Recognition of platinum-DNA adducts by HMGB1a

scientific article published on 14 September 2012

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

scientific article

Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition

scientific article published on 7 September 2017

Regioselectivity of Catechol O-Methyltransferase Confers Enhancement of Catalytic Activity

scientific article

Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases

scientific article published on 18 April 2010

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

scientific article published on 16 June 2010

Restoration of R117H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770

scientific article published on 8 July 2016

Rigid substructure search

scientific article

Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain

scientific article published on June 2010

Role of PIP2-Dependent Membrane Interactions in Vinculin Activation, Motility and Force Transmission

article

Ryanodine Receptor Pore Structure and Function

Scaling behavior and structure of denatured proteins

scientific article published in July 2005

Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation

scholarly article by Sagar D. Khare published in September 2005

Serotonin-induced hypersensitivity via inhibition of catechol O-methyltransferase activity

scientific article

Similarity and dissimilarity in correlations of genomic DNA

scholarly article

Simple but predictive protein models

article

Single-channel properties of skeletal muscle ryanodine receptor pore Δ4923FF4924 in two brothers with a lethal form of fetal akinesia

scientific article published on 17 February 2020

Single-molecule correlated chemical probing of RNA.

scientific article

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

scientific article published on 25 June 2002

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

scientific article published on 07 July 2017

Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling

scientific article published on 12 June 2019

Statistical analysis of SHAPE-directed RNA secondary structure modeling

scientific article published on 14 January 2013

Structural and dynamic determinants of protein-peptide recognition

scientific article

Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling

scientific article

Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase

scientific article

Structural basis for the sequence-dependent effects of platinum-DNA adducts

scientific article published on 02 March 2009

Structural basis for μ-opioid receptor binding and activation

scientific article

Structural determinants of skeletal muscle ryanodine receptor gating

scientific article published on 14 January 2013

Structural mechanism of S-adenosyl methionine binding to catechol O-methyltransferase

scientific article

Structure modeling of RNA using sparse NMR constraints

scientific article published on 20 November 2017

Studies of folding and misfolding using simplified models.

scientific article

Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics

scientific article published on June 2013

The Length Dependence of the PolyQ-mediated Protein Aggregation

scientific article published in Journal of Biological Chemistry

The N-terminal domain allosterically regulates cleavage and activation of the epithelial sodium channel.

scientific article

The architecture of the protein domain universe

article

The complex molecular biology of amyotrophic lateral sclerosis (ALS)

scientific article

The coordinated evolution of yeast proteins is constrained by functional modularity

article by Yiwen Chen & Nikolay V. Dokholyan published August 2006 in Trends in Genetics

The evolution dynamics of model proteins

article

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

scientific article

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

scientific article published on 22 November 2013

The path of DNA in the kinetochore

scientific article published on April 2006

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

scientific article

Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: computational approaches

scientific article (publication date: 2012)

Thermodynamic Stability of Histone H3 is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation

scientific article

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

scientific article

Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels

scientific article published on January 2009

Three-dimensional RNA structure refinement by hydroxyl radical probing

scientific article

Titr-DMD—A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework

scientific article published on 24 June 2021

Topological Determinants of Protein Domain Swapping

article published in 2006

Topological determinants of protein folding

scientific article

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal

scientific article

Transmembrane helical interactions in the CFTR channel pore.

scientific article

Two-input protein logic gate for computation in living cells

scientific article published on 16 November 2021

Tyrosine phosphorylation switching of a G protein substrate

scientific article

Uncertainty in oil production predicted by percolation theory

scholarly article

Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding

scientific article published on 17 May 2019

Understanding conserved amino acids in proteins

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

Using protein design for homology detection and active site searches

scientific article

Various miRNAs compensate the role of miR-122 on HCV replication

scientific article published on 23 June 2020

What is the protein design alphabet?

scientific article

iFold: a platform for interactive folding simulations of proteins

scientific article published in 2006

iFoldRNA v2: folding RNA with constraints

scientific article

iFoldRNA: three-dimensional RNA structure prediction and folding

scientific article

β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology

scientific article published on 19 July 2019

μ-Opioid receptor 6-transmembrane isoform: A potential therapeutic target for new effective opioids

scientific article published on 06 December 2014

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