(Q34300133)

1 August 2017

title

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics (English)

1 reference

1 August 2017

4

J Andrew McCammon

1 reference

1 August 2017

Levi C T Pierce

1

1 reference

1 August 2017

Romelia Salomon-Ferrer

series ordinal

2

1 reference

1 August 2017

Cesar Augusto F de Oliveira

series ordinal

3

1 reference

1 August 2017

Ross C Walker

series ordinal

5

1 reference

1 August 2017

publication date

27 July 2012

1 reference

Journal of Chemical Theory and Computation

1 August 2017

published in

1 reference

1 August 2017

volume

8

1 reference

1 August 2017

issue

9

1 reference

1 August 2017

page(s)

2997-3002

1 reference

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.

1 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Microsecond time-scale conformational exchange in proteins: using long molecular dynamics trajectory to simulate NMR relaxation dispersion data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Activation mechanism of the β2-adrenergic receptor

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Implementation of Accelerated Molecular Dynamics in NAMD

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

How does a drug molecule find its target binding site?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

SHIFTX2: significantly improved protein chemical shift prediction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Atomic-level characterization of the structural dynamics of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Everything you wanted to know about Markov State Models but were afraid to ask

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Targeting biomolecular flexibility with metadynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Common structural transitions in explicit-solvent simulations of villin headpiece folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Molecular dynamics simulations of membrane channels and transporters

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Accelerating molecular dynamic simulation on graphics processing units

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Membrane proteins: molecular dynamics simulations.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Combining experiment and simulation in protein folding: closing the gap for small model systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Calculation of protein-ligand binding affinities.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Sub-microsecond protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Designed replacement of an internal hydration water molecule in BPTI: structural and functional implications of a glycine-to-serine mutation.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Dynamics of folded proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Adaptive biasing force method for scalar and vector free energy calculations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Bio3d: an R package for the comparative analysis of protein structures.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Disulfide Bond Isomerization in Basic Pancreatic Trypsin Inhibitor: Multisite Chemical Exchange Quantified by CPMG Relaxation Dispersion and Chemical Shift Modeling

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Equilibrium Free Energies from Nonequilibrium Metadynamics

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3438784

Flooding inGROMACS: Accelerated barrier crossings in molecular dynamics

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22984356

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22984356

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT300284C

1 reference

release_ucw532cxijdm3es7b4dllvjula

1 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ucw532cxijdm3es7b4dllvjula

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

3438784

1 reference

1 August 2017

1 reference