(Q30554344)

19 August 2017

Population based reweighting of scaled molecular dynamics (English)

1 reference

molecular dynamics simulation

19 August 2017

0 references

4

J Andrew McCammon

1 reference

19 August 2017

William Sinko

1

1 reference

19 August 2017

Yinglong Miao

series ordinal

2

1 reference

19 August 2017

César Augusto F de Oliveira

series ordinal

3

1 reference

19 August 2017

language of work or name

English

0 references

publication date

11 July 2013

1 reference

Journal of Physical Chemistry B

19 August 2017

1 reference

19 August 2017

117

1 reference

19 August 2017

42

1 reference

19 August 2017

12759-12768

1 reference

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Atomic-level characterization of the structural dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Everything you wanted to know about Markov State Models but were afraid to ask

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

A black-box re-weighting analysis can correct flawed simulation data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Optimization by Simulated Annealing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

10 residue folded peptide designed by segment statistics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Stereochemistry of polypeptide chain configurations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Escaping free-energy minima

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Molecular dynamics simulations of biomolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Essential dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

The Energy Landscapes and Motions of Proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Integrating diffusion maps with umbrella sampling: application to alanine dipeptide.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Global energy minimization of alanine dipeptide via barrier function methods.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3808002

Folding Dynamics of 10-Residue β-Hairpin Peptide Chignolin

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23721224

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A statistical analysis of the precision of reweighting-based simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23721224

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Understanding protein flexibility through dimensionality reduction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23721224

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JP401587E

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

23721224

1 reference