(Q39943006)

15 September 2017

Progress and challenges in the automated construction of Markov state models for full protein systems (English)

1 reference

15 September 2017

0 references

4

Vijay S Pande

1 reference

15 September 2017

2

Kyle A Beauchamp

1 reference

15 September 2017

Gregory R Bowman

1

1 reference

15 September 2017

George Boxer

series ordinal

3

1 reference

15 September 2017

language of work or name

English

0 references

publication date

1 September 2009

1 reference

Journal of Chemical Physics

15 September 2017

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15 September 2017

131

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15 September 2017

124101

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15 September 2017

12

1 reference

Extracting Markov Models of Peptide Conformational Dynamics from Simulation Data

15 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Rapid equilibrium sampling initiated from nonequilibrium data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

The protein folding problem

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Transition networks for modeling the kinetics of conformational change in macromolecules

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Sub-microsecond protein folding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Hidden complexity of free energy surfaces for peptide (protein) folding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Small assemblies of unmodified amyloid beta-protein are the proximate neurotoxin in Alzheimer's disease

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Reaction coordinates of biomolecular isomerization

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Canonical dynamics: Equilibrium phase-space distributions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

VMD: visual molecular dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Structural insight into RNA hairpin folding intermediates

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Coarse master equations for peptide folding dynamics.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2766407

On the transition coordinate for protein folding

20 August 2018

1 reference

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

21 January 2018

1 reference

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Clustering to minimize the maximum intercluster distance

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.3216567

1 reference

release_422ymi4pebb6dnwemvb6jkbru4

15 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/422ymi4pebb6dnwemvb6jkbru4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

15 September 2017

1 reference