(Q36791225)

16 August 2017

REACH coarse-grained biomolecular simulation: transferability between different protein structural classes (English)

1 reference

16 August 2017

Kei Moritsugu

1

1 reference

16 August 2017

Jeremy C Smith

series ordinal

2

1 reference

16 August 2017

language of work or name

English

0 references

publication date

9 May 2008

1 reference

16 August 2017

1 reference

16 August 2017

95

1 reference

16 August 2017

4

1 reference

16 August 2017

1639-1648

1 reference

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

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Coarse-grained peptide modeling using a systematic multiscale approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Molecular dynamics simulations of the complete satellite tobacco mosaic virus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Coarse-grained modeling of the actin filament derived from atomistic-scale simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Scalable molecular dynamics with NAMD

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Coarse-grained normal mode analysis in structural biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Exploring global motions and correlations in the ribosome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Molecular mechanism of domain swapping in proteins: an analysis of slower motions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

29 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=2483758

Crystal structures of myoglobin-ligand complexes at near-atomic resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Stability and dynamics of virus capsids described by coarse-grained modeling

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Modeling real dynamics in the coarse-grained representation of condensed phase systems.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Analysis of domain motions by approximate normal mode calculations

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

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

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2483758

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis

4 December 2018

1 reference

12 December 2020

Langevin model of the temperature and hydration dependence of protein vibrational dynamics

1 reference

12 December 2020

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

12 December 2020

Exploring the Essential Dynamics of B-DNA

1 reference

12 December 2020

10.1529/BIOPHYSJ.108.131714

Identifiers

DOI

1 reference

16 August 2017

1 reference

16 August 2017

PubMed publication ID

18469078

1 reference