iGNM: a database of protein functional motions based on Gaussian Network Model. (Q30350647)

13 November 2017

iGNM: a database of protein functional motions based on Gaussian Network Model. (English)

1 reference

13 November 2017

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7

Ivet Bahar

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author name string

Lee-Wei Yang

1

1 reference

13 November 2017

Xiong Liu

2

1 reference

13 November 2017

Christopher J Jursa

3

1 reference

13 November 2017

Mark Holliman

4

1 reference

13 November 2017

A J Rader

5

1 reference

13 November 2017

Hassan A Karimi

6

1 reference

13 November 2017

language of work or name

English

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publication date

28 April 2005

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13 November 2017

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13 November 2017

21

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13 November 2017

13

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13 November 2017

2978-2987

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Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

13 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

How does protein architecture facilitate the transduction of ATP chemical-bond energy into mechanical work? The cases of nitrogenase and ATP binding-cassette proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Mining frequent patterns in protein structures: a study of protease families.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

New advances in normal mode analysis of supermolecular complexes and applications to structural refinement

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

ProMode: a database of normal mode analyses on protein molecules with a full-atom model.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Molecular dynamics simulations of peptides and proteins with amplified collective motions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Normal mode analysis with simplified models to investigate the global dynamics of biological systems.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

MolMovDB: analysis and visualization of conformational change and structural flexibility

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Conformational change of proteins arising from normal mode calculations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Anisotropy of fluctuation dynamics of proteins with an elastic network model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Ligand-induced changes in the structure and dynamics of a human class Mu glutathione S-transferase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Microscopic stability of cold shock protein A examined by NMR native state hydrogen exchange as a function of urea and trimethylamine N-oxide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

3 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Investigating protein dynamics in collective coordinate space

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Cooperative fluctuations and subunit communication in tryptophan synthase.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Identification of kinetically hot residues in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Analysis of catalytic residues in enzyme active sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Topological thermal instability and length of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Statistical Thermodynamics of Random Networks [and Discussion]

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Analysis of domain motions by approximate normal mode calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Automatic domain decomposition of proteins by a Gaussian Network Model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Maturation dynamics of bacteriophage HK97 capsid.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

On the potential of normal-mode analysis for solving difficult molecular-replacement problems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Global ribosome motions revealed with elastic network model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTI469

Building-block approach for determining low-frequency normal modes of macromolecules.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1752228

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15860562

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Universal behavior of localization of residue fluctuations in globular proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15860562

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Hinge-bending motions in annexins: molecular dynamics and essential dynamics of apo-annexin V and of calcium bound annexin V and I

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15860562

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTI469

1 reference

journals/bioinformatics/YangLJHRKB05

13 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

13 November 2017

1 reference