(Q36944336)

17 August 2017

Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations (English)

1 reference

17 August 2017

1 reference

2

1 reference

17 August 2017

Mahmoud Moradi

1

0 references

publication date

17 May 2013

1 reference

Journal of Physical Chemistry Letters

17 August 2017

1 reference

17 August 2017

4

1 reference

17 August 2017

1882-1887

1 reference

17 August 2017

11

1 reference

λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Conformations and free energy landscapes of polyproline peptides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Scalable molecular dynamics with NAMD

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Escaping free-energy minima

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Energetics of glycerol conduction through aquaglyceroporin GlpF.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

How does a system respond when driven away from thermal equilibrium?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Molecular dynamics study of unbinding of the avidin-biotin complex

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Local elevation: a method for improving the searching properties of molecular dynamics simulation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

PPII propensity of multiple-guest amino acids in a proline-rich environment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Adaptively biased molecular dynamics for free energy calculations

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Side-chain effects on peptidyl-prolyl cis/trans isomerisation.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Equilibrium Free Energies from Nonequilibrium Metadynamics

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688312

Optimized free energies from bidirectional single-molecule force spectroscopy

4 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23795244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

DNA Bending through Roll Angles Is Independent of Adjacent Base Pairs

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23795244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Efficient extraction of free energy profiles from nonequilibrium experiments

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23795244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JZ400816X

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

PMCID

3688312