(Q37282402)

19 August 2017

Protein elastic network models and the ranges of cooperativity (English)

1 reference

19 August 2017

3

Robert L Jernigan

1 reference

19 August 2017

Lei Yang

1

1 reference

19 August 2017

Guang Song

series ordinal

2

1 reference

19 August 2017

language of work or name

English

0 references

publication date

14 July 2009

1 reference

Proceedings of the National Academy of Sciences of the United States of America

19 August 2017

1 reference

19 August 2017

106

1 reference

19 August 2017

30

1 reference

19 August 2017

12347-12352

1 reference

Application of elastic network models to proteins in the crystalline state

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Deriving protein dynamical properties from weighted protein contact number.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Protein structural variation in computational models and crystallographic data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

The gaussian network model: precise prediction of residue fluctuations and application to binding problems

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Protein flexibility and rigidity predicted from sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Improved amino acid flexibility parameters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Flexibility and packing in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Anisotropy of fluctuation dynamics of proteins with an elastic network model

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Proteins with similar architecture exhibit similar large-scale dynamic behavior

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

6 September 2017

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=2718344

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Dynamics of folded proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Efficient generation of feasible pathways for protein conformational transitions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

vGNM: a better model for understanding the dynamics of proteins in crystals

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Comparisons of experimental and computed protein anisotropic temperature factors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

How well can we understand large-scale protein motions using normal modes of elastic network models?

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Rigid-cluster models of conformational transitions in macromolecular machines and assemblies

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

An elastic network model of HK97 capsid maturation

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Conformational change of proteins arising from normal mode calculations

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Comparing anisotropic displacement parameters in protein structures

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Structural flexibility in proteins: impact of the crystal environment

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Prediction of protein B-factors using multi-class bounded SVM.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Loop motions of triosephosphate isomerase observed with elastic networks.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Prediction of protein B-factor profiles.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Global ribosome motions revealed with elastic network model

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Protein flexibility and intrinsic disorder

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Analysis of domain motions by approximate normal mode calculations.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2718344

Improved simulation of liquid water by molecular dynamics

3 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0902159106

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0902159106

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0902159106

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0902159106

Harmonicity in slow protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0902159106

Accuracy of protein flexibility predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0902159106

On the interrelationship between atomic displacement parameters (ADPs) and coordinates in protein structures

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19617554

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19617554

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

An enhanced elastic network model to represent the motions of domain-swapped proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19617554

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0902159106

1 reference

19 August 2017

0 references

1 reference

19 August 2017

PubMed publication ID

19617554

1 reference