Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations (Q35661992)

9 August 2017

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

1 reference

9 August 2017

4

J Andrew McCammon

1 reference

9 August 2017

William Sinko

1

1 reference

PubMed ID

22241967

9 August 2017

César Augusto F de Oliveira

series ordinal

2

1 reference

PubMed ID

22241967

9 August 2017

Levi C T Pierce

series ordinal

3

1 reference

9 August 2017

21 November 2011

1 reference

Journal of Chemical Theory and Computation

9 August 2017

1 reference

9 August 2017

8

1 reference

9 August 2017

1

1 reference

9 August 2017

17-23

1 reference

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.

9 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case 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=3254191

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Host-guest complexes with protein-ligand-like affinities: computational analysis and design

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

On the application of accelerated molecular dynamics to liquid water simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Elasticity of peptide omega bonds

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Molecular dynamics simulations of biomolecules

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Global energy minimization of alanine dipeptide via barrier function methods.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Enhanced conformational space sampling improves the prediction of chemical shifts in proteins

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Essential energy space random walks to accelerate molecular dynamics simulations: convergence improvements via an adaptive-length self-healing strategy

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Partitioning the loss in vancomycin binding affinity for D-Ala-D-Lac into lost H-bond and repulsive lone pair contributions

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3254191

Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy

25 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22241967

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/22241967

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Rigorous Free Energy Calculations in Structure-Based Drug Design.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22241967

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT200615K

1 reference

9 August 2017

1 reference

9 August 2017

1 reference

PubMed ID

22241967