(Q30539212)

17 September 2017

Enhanced modeling via network theory: Adaptive sampling of Markov state models (English)

1 reference

17 September 2017

3

Vijay S Pande

1 reference

17 September 2017

Gregory R Bowman

1

1 reference

PMC publication ID

3637129

17 September 2017

Daniel L Ensign

series ordinal

2

1 reference

17 September 2017

1 January 2010

1 reference

Journal of Chemical Theory and Computation

17 September 2017

1 reference

17 September 2017

6

1 reference

17 September 2017

3

1 reference

17 September 2017

787-794

1 reference

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

17 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Rapid equilibrium sampling initiated from nonequilibrium data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Long-timescale molecular dynamics simulations of protein structure and function.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

The automation of science.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Transition networks for modeling the kinetics of conformational change in macromolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

An experimental survey of the transition between two-state and downhill protein folding scenarios

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

COMPUTING: Screen Savers of the World Unite!

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Toward high-resolution de novo structure prediction for small proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

On the simulation of protein folding by short time scale molecular dynamics and distributed computing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Solution NMR structures of IgG binding domains with artificially evolved high levels of sequence identity but different folds

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Computing time scales from reaction coordinates by milestoning.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637129

Multiple state transition path sampling

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23626502

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mathematical analysis of coupled parallel simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23626502

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT900620B

1 reference

17 September 2017

1 reference

PMC publication ID

3637129

17 September 2017

PubMed publication ID

23626502

1 reference

PMC publication ID

3637129