(Q42553727)

2 November 2017

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis (English)

1 reference

2 November 2017

1 reference

1 reference

1 reference

1

1 reference

2 November 2017

Patrice Koehl

3

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author name string

Cyril Azuara

series ordinal

2

1 reference

PMCID

1538881

2 November 2017

Marc Delarue

series ordinal

4

1 reference

PMCID

1538881

2 November 2017

language of work or name

English

0 references

publication date

1 July 2006

1 reference

2 November 2017

Nucleic Acids Research

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2 November 2017

34

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2 November 2017

W52-6

1 reference

2 November 2017

Web Server issue

1 reference

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

2 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

Accounting for global protein deformability during protein-protein and protein-ligand docking

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

GROMACS: fast, flexible, and free

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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=1538881

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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=1538881

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=1538881

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=1538881

Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

The CCP4 suite: programs for protein crystallography

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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=1538881

On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural 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=1538881

Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

ProMode: a database of normal mode analyses on protein molecules with a full-atom 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=1538881

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

Efficient generation of feasible pathways for protein conformational transitions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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=1538881

ATP-bound states of GroEL captured by 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=1538881

Conformational change of proteins arising from normal mode calculations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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=1538881

Representing receptor flexibility in ligand docking through relevant normal modes.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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=1538881

Analysis of domain motions by approximate normal mode calculations.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

The direct rotation function: rotational Patterson correlation search applied to molecular replacement

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

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

1 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1538881

1 December 2018

Identifiers

DOI

10.1093/NAR/GKL082

1 reference

journals/nar/LindahlAKD06

2 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 November 2017

1 reference

PMCID

1538881