(Q33508733)

27 July 2017

title

Rapid equilibrium sampling initiated from nonequilibrium data (English)

1 reference

27 July 2017

4

Vijay S Pande

1 reference

27 July 2017

Xuhui Huang

1

1 reference

27 July 2017

Gregory R Bowman

series ordinal

2

1 reference

27 July 2017

Sergio Bacallado

series ordinal

3

1 reference

27 July 2017

language of work or name

English

0 references

publication date

29 September 2009

1 reference

Proceedings of the National Academy of Sciences of the United States of America

27 July 2017

published in

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27 July 2017

volume

106

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27 July 2017

issue

47

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27 July 2017

page(s)

19765-19769

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Using generalized ensemble simulations and Markov state models to identify conformational states

27 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Simulated tempering yields insight into the low-resolution Rosetta scoring functions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Structural insight into RNA hairpin folding intermediates

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Transition networks for modeling the kinetics of conformational change in macromolecules

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Observation of noncooperative folding thermodynamics in simulations of 1BBL.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Simulating replica exchange simulations of protein folding with a kinetic network model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

DNA folding and melting observed in real time redefine the energy landscape

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Folding of proteins with diverse folds

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Is hairpin formation in single-stranded polynucleotide diffusion-controlled?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Does water play a structural role in the folding of small nucleic acids?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

New Monte Carlo algorithms for protein folding.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Simple model of protein folding kinetics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

Tetraloops and RNA folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2785240

The free energy landscape for beta hairpin folding in explicit water

28 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Convergence of replica exchange molecular dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Computing time scales from reaction coordinates by milestoning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Coarse master equations for peptide folding dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Probability distributions of molecular observables computed from Markov models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0909088106

Exploring the energy landscape of a small RNA hairpin

21 January 2018

1 reference

12 December 2020

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

1 reference

12 December 2020

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

1 reference

12 December 2020

Optimizing replica exchange moves for molecular dynamics

1 reference

12 December 2020

Dynamics and optimal number of replicas in parallel tempering simulations

1 reference

12 December 2020

How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach

1 reference

12 December 2020

A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0909088106

1 reference

27 July 2017

0 references

1 reference

27 July 2017

1 reference