(Q41859162)

13 October 2017

Revisiting and computing reaction coordinates with Directional Milestoning (English)

1 reference

13 October 2017

Serdal Kirmizialtin

1

1 reference

13 October 2017

Ron Elber

series ordinal

2

1 reference

13 October 2017

language of work or name

English

0 references

publication date

18 April 2011

1 reference

Journal of Physical Chemistry A

13 October 2017

1 reference

13 October 2017

115

1 reference

13 October 2017

23

1 reference

13 October 2017

6137-6148

1 reference

Atomic-level characterization of the structural dynamics of proteins

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Maximum Flux Transition Paths of Conformational Change

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Milestoning without a Reaction Coordinate

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Atomically detailed simulation of the recovery stroke in myosin by Milestoning

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Kinetics of helix unfolding: molecular dynamics simulations with milestoning

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Transition-path theory and path-finding algorithms for the study of rare events

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Ion conduction and selectivity in K(+) channels

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS"

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

The double helix: a tale of two puckers

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

On the assumptions underlying milestoning

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Rate constant and reaction coordinate of Trp-cage folding in explicit water

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Coarse master equations for peptide folding dynamics.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Extensions to the likelihood maximization approach for finding reaction coordinates.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Obtaining reaction coordinates by likelihood maximization.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Automatic method for identifying reaction coordinates in complex systems.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

String method in collective variables: minimum free energy paths and isocommittor surfaces.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Efficient computation of the first passage time distribution of the generalized master equation by steady-state relaxation.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Simulating rare events in equilibrium or nonequilibrium stochastic systems.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Rate constants for diffusive processes by partial path sampling.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Computing time scales from reaction coordinates by milestoning.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Kinetics of cytochrome C folding: atomically detailed simulations

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3116089

Nanosecond relaxation processes in aqueous mononucleoside solutions

18 August 2018

1 reference

12 December 2020

Exploring the energy landscape of a small RNA hairpin

1 reference

12 December 2020

Calculation of Point-to-Point Short-Time and Rare Trajectories with Boundary Value Formulation

1 reference

12 December 2020

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP111093C

1 reference

13 October 2017

1 reference

13 October 2017

PubMed publication ID

21500798

1 reference