(Q37610801)

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Coarse-grained models reveal functional dynamics--II. Molecular dynamics simulation at the coarse-grained level--theories and biological applications.

scientific article published on 05 March 2008

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

1 reference

Europe PubMed Central

Coarse-grained models reveal functional dynamics--II. Molecular dynamics simulation at the coarse-grained level--theories and biological applications (English)

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

author name string

Choon-Peng Chng

1

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

Lee-Wei Yang

2

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

publication date

5 March 2008

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

Bioinformatics and Biology Insights

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

2

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

171-185

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

Coarse-grained models of protein folding: toy models or predictive tools?

1 reference

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23 August 2017

The MARTINI force field: coarse grained model for biomolecular simulations

1 reference

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23 August 2017

From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

1 reference

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23 August 2017

HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics

1 reference

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23 August 2017

Multiscale modeling of biomolecular systems: in serial and in parallel

1 reference

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23 August 2017

Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations.

1 reference

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1 reference

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

1 reference

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

1 reference

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23 August 2017

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

1 reference

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23 August 2017

Coarse grained protein-lipid model with application to lipoprotein particles

1 reference

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23 August 2017

Insertion and assembly of membrane proteins via simulation.

1 reference

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23 August 2017

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

1 reference

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

1 reference

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23 August 2017

Scalable molecular dynamics with NAMD

1 reference

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23 August 2017

Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment

1 reference

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23 August 2017

Coarse-grained models for proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

23 August 2017

Direct molecular dynamics observation of protein folding transition state ensemble

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

23 August 2017

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations

1 reference

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23 August 2017

The structure of glutamine-binding protein complexed with glutamine at 1.94 A resolution: comparisons with other amino acid binding proteins

1 reference

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23 August 2017

Computer simulation of protein folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

23 August 2017

A simplified representation of protein conformations for rapid simulation of protein folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

23 August 2017

The origins of asymmetry in the folding transition states of protein L and protein G.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

6 September 2017

Discrete molecular dynamics studies of the folding of a protein-like model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

25 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

25 June 2018

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions

1 reference

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25 June 2018

Protein conformational transitions explored by mixed elastic network models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735960

1 September 2018

Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations

1 reference

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

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Multiscale modeling of nucleosome dynamics

1 reference

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Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

1 reference

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Deriving effective mesoscale potentials from atomistic simulations.

1 reference

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Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

1 reference

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Slow Conformational Dynamics and Unfolding of the Calmodulin C-Terminal Domain

1 reference

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3 December 2018

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

1 reference

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1 reference

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1 reference

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3 December 2018

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1 reference

https://pubmed.ncbi.nlm.nih.gov/19812774

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function

1 reference

https://pubmed.ncbi.nlm.nih.gov/19812774

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.4137/BBI.S459

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19812774%20AND%20SRC:MED&resulttype=core&format=json

9 February 2020

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