(Q35012592)

25247823

5 August 2017

title

The adaptive biasing force method: everything you always wanted to know but were afraid to ask (English)

1 reference

5 August 2017

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Tony Lelièvre

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

2

James C Gumbart

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

author name string

Jeffrey Comer

1

1 reference

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3 June 2020

Andrew Pohorille

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Christophe Chipot

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

language of work or name

English

0 references

publication date

7 October 2014

1 reference

25247823

Journal of Physical Chemistry B

5 August 2017

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

volume

119

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

issue

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

page(s)

1129-1151

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

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

3 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Efficient determination of protein-protein standard binding free energies from first principles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Standard binding free energies from computer simulations: What is the best strategy?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

A Bayesian inference scheme to extract diffusivity and potential fields from confined single-molecule trajectories

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Theory of binless multi-state free energy estimation with applications to protein-ligand binding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Diffusion models of protein folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Scalable molecular dynamics with NAMD

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Reaction coordinates and rates from transition paths

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Escaping free-energy minima

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Molecular dynamics study of unbinding of the avidin-biotin complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Diffusion in a rough potential

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Diffusive Models of Membrane Permeation with Explicit Orientational Freedom.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Calculation of Lipid-Bilayer Permeabilities Using an Average Force.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Recovering position-dependent diffusion from biased molecular dynamics simulations.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Calculating diffusion and permeability coefficients with the oscillating forward-reverse method.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Good practices in free-energy calculations

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Free energy calculations: an efficient adaptive biasing potential method.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Permeation of membranes by ribose and its diastereomers.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Multidimensional Langevin modeling of biomolecular dynamics

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Binless estimation of the potential of mean force.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Adaptive biasing force method for scalar and vector free energy calculations

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Adaptively biased molecular dynamics for free energy calculations

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Computation of free energy profiles with parallel adaptive dynamics.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Automatic method for identifying reaction coordinates in complex systems.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Optimal estimates of free energies from multistate nonequilibrium work data.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Exploring the free-energy landscape of a short peptide using an average force

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Overcoming free energy barriers using unconstrained molecular dynamics simulations

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Assessing the efficiency of free energy calculation methods

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Theory of a systematic computational error in free energy differences.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Replica Monte Carlo simulation of spin glasses.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Equilibrium Free Energies from Nonequilibrium Metadynamics

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4306294

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

9 December 2018

1 reference

12 December 2020

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations

1 reference

12 December 2020

Energetics of ion transport in a peptide nanotube

1 reference

12 December 2020

Molecular dynamics study of the inclusion of cholesterol into cyclodextrins

1 reference

12 December 2020

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP506633N

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

25247823

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25247823%20AND%20SRC:MED&resulttype=core&format=json