(Q33603629)

28 July 2017

title

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

1 reference

28 July 2017

main subject

distributed computing

0 references

1 reference

3

Vijay S Pande

1 reference

28 July 2017

Xuhui Huang

1

1 reference

28 July 2017

Gregory R Bowman

series ordinal

2

1 reference

28 July 2017

language of work or name

English

0 references

publication date

1 May 2008

1 reference

Journal of Chemical Physics

28 July 2017

published in

1 reference

28 July 2017

volume

128

1 reference

28 July 2017

issue

20

1 reference

28 July 2017

page(s)

205106

1 reference

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

28 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=2809694

Asynchronous replica exchange for molecular simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

COMPUTING: Screen Savers of the World Unite!

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

21 June 2018

Serial replica exchange

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Local structure formation in simulations of two small proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Simulations of the role of water in the protein-folding mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Trp-cage: Folding free energy landscape in explicit water

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Absolute comparison of simulated and experimental protein-folding dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

The free energy landscape for beta hairpin folding in explicit water

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

New Monte Carlo algorithms for protein folding.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Canonical dynamics: Equilibrium phase-space distributions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Comparison of NH exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Fast events in protein folding: helix melting and formation in a small peptide.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2809694

Conformational sampling via a self-regulating effective energy surface.

21 June 2018

1 reference

Nanotube confinement denatures protein helices.

21 January 2018

1 reference

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

Parallel tempering simulations of HP-36.

21 January 2018

1 reference

Choosing weights for simulated tempering

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

1 reference

Bayesian update method for adaptive weighted sampling

21 January 2018

1 reference

Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

21 January 2018

1 reference

Optimal allocation of replicas in parallel tempering simulations.

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

Replica-exchange simulated tempering method for simulations of frustrated systems

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.2908251

1 reference

28 July 2017

1 reference

28 July 2017

1 reference