Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble (Q35639961)

9 August 2017

Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble (English)

1 reference

9 August 2017

Xiongwu Wu

1

1 reference

PubMed ID

22128922

9 August 2017

Bernard R Brooks

series ordinal

2

1 reference

PubMed ID

22128922

9 August 2017

language of work or name

English

0 references

publication date

1 November 2011

1 reference

Journal of Chemical Physics

9 August 2017

1 reference

9 August 2017

135

1 reference

9 August 2017

20

1 reference

9 August 2017

204101

1 reference

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

9 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Interaction of an ionic complementary peptide with a hydrophobic graphite surface

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

CHARMM: the biomolecular simulation program

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Self-guided Langevin dynamics study of regulatory interactions in NtrC.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Folding of immunogenic peptide fragments of proteins in water solution. II. The nascent helix

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3248022

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange.

12 July 2018

1 reference

Simulation of peptide folding with explicit water--a mean solvation method.

21 January 2018

1 reference

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

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

21 January 2018

1 reference

Adaptive biasing force method for scalar and vector free energy calculations

21 January 2018

1 reference

Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.

21 January 2018

1 reference

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

21 January 2018

1 reference

The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis

21 January 2018

1 reference

Characterizing the denatured state of human prion 121-230

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22128922

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22128922

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.3662489

1 reference

9 August 2017

1 reference

9 August 2017

1 reference

PubMed ID

22128922