(Q41820785)

12 October 2017

Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules (English)

1 reference

12 October 2017

1 reference

2

Arieh Warshel

1 reference

12 October 2017

Anatoly Dryga

1

1 reference

PMCID

2948080

12 October 2017

language of work or name

English

0 references

publication date

1 October 2010

1 reference

Journal of Physical Chemistry B

12 October 2017

1 reference

12 October 2017

114

1 reference

12 October 2017

39

1 reference

12 October 2017

12720-12728

1 reference

Role of conformation transitions in adenylate kinase

12 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Catching a protein in the act.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Enzyme millisecond conformational dynamics do not catalyze the chemical step

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Exploring the role of large conformational changes in the fidelity of DNA polymerase beta

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Modeling electrostatic effects in proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Free energy surfaces from single-molecule force spectroscopy

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Calculating potentials of mean force from steered molecular dynamics simulations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Molecular dynamics simulations of biological reactions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Dynamics of biochemical and biophysical reactions: insight from computer simulations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Steered molecular dynamics and mechanical functions of proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Boundary conditions for- single-ion diffusion

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Bicycle-pedal model for the first step in the vision process

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Generalized Langevin models of molecular dynamics simulations with applications to ion channels.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Reconstructing potentials of mean force from short steered molecular dynamics simulations of Vpu from HIV-1.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Conformational transitions in adenylate kinase. Allosteric communication reduces misligation

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Exploring the origin of the ion selectivity of the KcsA potassium channel

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Simulations of ion current in realistic models of ion channels: the KcsA potassium channel

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2948080

Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity

18 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20836533

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

On the Theory of the Brownian Motion

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

Replica-exchange molecular dynamics method for protein folding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

The fluctuation-dissipation theorem

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

On the use of local diffusion models for path ensemble averaging in potential of mean force computations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

Nonequilibrium Equality for Free Energy Differences

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

Stochastic Problems in Physics and Astronomy

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP1056122

Identifiers

DOI

10.1021/JP1056122

1 reference

12 October 2017

1 reference

12 October 2017

1 reference

PMCID

2948080