(Q35346073)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

title

Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations (English)

1 reference

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21 February 2020

2

1 reference

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21 February 2020

Alan Grossfield

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

author name string

Tod D Romo

series ordinal

1

1 reference

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21 February 2020

publication date

18 October 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

Journal of Computational Chemistry

21 February 2020

published in

1 reference

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21 February 2020

volume

35

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

issue

32

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

page(s)

2305-2318

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers.

21 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Structure-based simulations reveal concerted dynamics of GPCR activation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Elastic Network Models are Robust to Variations in Formalism

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Quantifying uncertainty and sampling quality in biomolecular simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Protein elastic network models and the ranges of cooperativity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

On the structural convergence of biomolecular simulations by determination of the effective sample size

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Ensemble-based convergence analysis of biomolecular trajectories

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

GROMACS: fast, flexible, and free

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

The Amber biomolecular simulation programs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Anisotropy of fluctuation dynamics of proteins with an elastic network model

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

VMD: visual molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

A sampling problem in molecular dynamics simulations of macromolecules

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4227929

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

12 July 2018

1 reference

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories.

21 January 2018

1 reference

An extended set of FORTRAN basic linear algebra subprograms

21 January 2018

1 reference

A set of level 3 basic linear algebra subprograms

21 January 2018

1 reference

Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

21 January 2018

1 reference

Convergence of sampling in protein simulations.

21 January 2018

1 reference

Assessing equilibration and convergence in biomolecular simulations

21 January 2018

1 reference

Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements.

21 January 2018

1 reference

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

21 January 2018

1 reference

Harmonicity in slow protein dynamics

21 January 2018

1 reference

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

21 January 2018

1 reference

ST-analyzer: a web-based user interface for simulation trajectory analysis

21 January 2018

1 reference

12 December 2020

Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation

1 reference

12 December 2020

1 reference

12 December 2020

Software news and updates. Carma: a molecular dynamics analysis program

1 reference

12 December 2020

Validating and improving elastic network models with molecular dynamics simulations

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

Convergence of molecular dynamics simulations of membrane proteins

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.23753

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

DBLP publication ID

journals/jcc/RomoLG14

1 reference

DBLP Dataset 2021-01-02

release_a7cjomfedbeqrp3amwhb4b4uve

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/a7cjomfedbeqrp3amwhb4b4uve

24 November 2022

mapped directly with Wikidata item

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25327784%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

PubMed publication ID

25327784

1 reference