(Q37375604)

20 August 2017

Finding transition pathways using the string method with swarms of trajectories (English)

1 reference

20 August 2017

Albert C Pan

1

1 reference

20 August 2017

Deniz Sezer

series ordinal

2

1 reference

20 August 2017

Benoît Roux

series ordinal

3

1 reference

20 August 2017

language of work or name

English

0 references

publication date

22 February 2008

1 reference

Journal of Physical Chemistry B

20 August 2017

1 reference

20 August 2017

112

1 reference

20 August 2017

11

1 reference

20 August 2017

3432-3440

1 reference

Coarse-grained free energy functions for studying protein conformational changes: a double-well network model

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Long-timescale simulation methods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Reaction coordinates and rates from transition paths

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Escaping free-energy minima

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Steered molecular dynamics and mechanical functions of proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Reaction coordinates of biomolecular isomerization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Structure of a transiently phosphorylated switch in bacterial signal transduction

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Protein conformational transitions explored by mixed elastic network models.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Simplified and improved string method for computing the minimum energy paths in barrier-crossing events.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Sampling diffusive transition paths

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

From A to B in free energy space.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Automatic method for identifying reaction coordinates in complex systems.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Finite temperature string method for the study of rare events.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Exploring the free-energy landscape of a short peptide using an average force

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Energetics of ion conduction through the K+ channel.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2757167

Two-state allosteric behavior in a single-domain signaling protein

3 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18290641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Temperature-Dependent Probabilistic Roadmap Algorithm for Calculating Variationally Optimized Conformational Transition Pathways.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18290641

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JP0777059

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

18290641

1 reference