oGNM: online computation of structural dynamics using the Gaussian Network Model (Q42552418)

2 November 2017

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

1 reference

2 November 2017

7

Ivet Bahar

0 references

author name string

Lee-Wei Yang

1

1 reference

2 November 2017

A J Rader

2

1 reference

2 November 2017

Xiong Liu

3

1 reference

2 November 2017

Cristopher Jon Jursa

4

1 reference

2 November 2017

Shann Ching Chen

5

1 reference

2 November 2017

Hassan A Karimi

6

1 reference

2 November 2017

language of work or name

English

0 references

publication date

1 July 2006

1 reference

2 November 2017

Nucleic Acids Research

1 reference

2 November 2017

34

1 reference

2 November 2017

W24-31

1 reference

2 November 2017

Web Server issue

1 reference

Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies

2 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Intrinsic dynamics of an enzyme underlies catalysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Coarse-grained normal mode analysis in structural biology

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Comparison of mode analyses at different resolutions applied to nucleic acid systems

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

WEBnm@: a web application for normal mode analyses of proteins

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Exploring the common dynamics of homologous proteins. Application to the globin family.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

An analysis of core deformations in protein superfamilies

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

A comparative study of motor-protein motions by using a simple elastic-network model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

How to describe protein motion without amino acid sequence and atomic coordinates.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

28 May 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=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Global ribosome motions revealed with elastic network model.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

PQS: a protein quaternary structure file server.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538811

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved

16 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16845002

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL084

1 reference

journals/nar/YangRLJCKB06

2 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 November 2017

1 reference