(Q33619016)

28 July 2017

Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology (English)

1 reference

28 July 2017

1

0 references

Ivet Bahar

series ordinal

2

object named as

Ivet Bahar

0 references

publication date

17 June 2010

1 reference

PLOS Computational Biology

28 July 2017

1 reference

28 July 2017

6

1 reference

28 July 2017

6

1 reference

28 July 2017

e1000816

1 reference

Creative Commons Attribution 4.0 International

28 July 2017

start time

17 June 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Conformational averaging in structural biology: issues, challenges and computational solutions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Observing biological dynamics at atomic resolution using NMR.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

The role of dynamic conformational ensembles in biomolecular recognition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Protein elastic network models and the ranges of cooperativity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Systematic multiscale parameterization of heterogeneous elastic network models of proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

oGNM: online computation of structural dynamics using the Gaussian Network Model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Weak pairwise correlations imply strongly correlated network states in a neural population

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Can conformational change be described by only a few normal modes?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Intrinsic dynamics of an enzyme underlies catalysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Simultaneous determination of protein structure and dynamics.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Announcing the worldwide Protein Data Bank

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Dynamics of proteins in crystals: comparison of experiment with simple models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Conformational change of proteins arising from normal mode calculations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Anisotropy of fluctuation dynamics of proteins with an elastic network model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Sequence evolution and the mechanism of protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Knowledge-based interaction potentials for proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Identification of kinetically hot residues in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Structure-derived potentials and protein simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

How optimization of potential functions affects protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Navigating the folding routes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Funnels, pathways, and the energy landscape of protein folding: a synthesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Spin glasses and the statistical mechanics of protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Protein tertiary structure recognition using optimized Hamiltonians with local interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

A dynamic view of enzyme catalysis

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Analysis of domain motions by approximate normal mode calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Information Theory and Statistical Mechanics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Information Theory and Statistical Mechanics. II

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

The precision of NMR structure ensembles revisited.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Inferential structure determination.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2887458

Harmonicity in slow protein dynamics

30 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Inference of the solvation energy parameters of amino acids using maximum entropy approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

COCO: A simple tool to enrich the representation of conformational variability in NMR structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000816

Analysis of domain motions in large proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20585542

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Allostery in a coarse-grained model of protein dynamics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20585542

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000816

1 reference

28 July 2017

journals/ploscb/LezonB10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

28 July 2017

1 reference

PubMed ID

20585542