(Q36432482)

14 August 2017

A generic force field for protein coarse-grained molecular dynamics simulation (English)

1 reference

14 August 2017

0 references

Junfeng Gu

1

1 reference

14 August 2017

Fang Bai

series ordinal

2

1 reference

14 August 2017

Honglin Li

series ordinal

3

1 reference

14 August 2017

Xicheng Wang

series ordinal

4

1 reference

14 August 2017

language of work or name

English

0 references

publication date

8 November 2012

1 reference

International Journal of Molecular Sciences

14 August 2017

1 reference

14 August 2017

13

1 reference

14 August 2017

11

1 reference

14 August 2017

14451-14469

1 reference

Creative Commons Attribution 4.0 International

14 August 2017

start time

8 November 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?

1 reference

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

A force field for virtual atom molecular mechanics of proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Long-timescale molecular dynamics simulations of protein structure and function.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Molecular dynamics simulations of membrane channels and transporters

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Membrane-protein interactions in a generic coarse-grained model for lipid bilayers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Four-scale description of membrane sculpting by BAR domains

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Membrane proteins: molecular dynamics simulations.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Biomolecular simulation: historical picture and future perspectives.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Coarse-grained peptide modeling using a systematic multiscale approach

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

High performance computing in biology: multimillion atom simulations of nanoscale systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Molecular dynamics: survey of methods for simulating the activity of proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Coarse grained protein-lipid model with application to lipoprotein particles

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Coarse-grained models for proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Computational analysis of sequence selection mechanisms.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

30 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=3509591

Dynamics of folded proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

Generic coarse-grained model for protein folding and aggregation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

28 June 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS131114451

Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS131114451

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS131114451

A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS131114451

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS131114451

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS131114451

Deriving effective mesoscale potentials from atomistic simulations.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3509591

A coarse grained model for the dynamics of flap opening in HIV-1 protease

21 September 2018

1 reference

https://api.crossref.org/works/10.3390%2FIJMS131114451

Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds

21 January 2018

1 reference

12 December 2020

Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains

1 reference

12 December 2020

Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations

1 reference

12 December 2020

A coarse-grained protein-protein potential derived from an all-atom force field

1 reference

12 December 2020

Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides

1 reference

12 December 2020

PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides.

1 reference

12 December 2020

Identifiers

DOI

10.3390/IJMS131114451

1 reference

14 August 2017

1 reference

14 August 2017

PubMed publication ID

23203075

1 reference