MDAnalysis: a toolkit for the analysis of molecular dynamics simulations (Q33875319)

29 July 2017

title

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations (English)

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29 July 2017

author name string

Naveen Michaud-Agrawal

1

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29 July 2017

Elizabeth J Denning

2

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Thomas B Woolf

3

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Oliver Beckstein

4

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publication date

15 April 2011

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Journal of Computational Chemistry

29 July 2017

published in

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volume

32

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issue

10

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page(s)

2319-2327

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

Protein thermostability calculations using alchemical free energy simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

Fast determination of the optimal rotational matrix for macromolecular superpositions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

LOOS: an extensible platform for the structural analysis of simulations.

28 July 2018

1 reference

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Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

CHARMM: the biomolecular simulation program

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

MD-tracks: a productive solution for the advanced analysis of molecular dynamics and Monte Carlo simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

The Amber biomolecular simulation programs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

Rapid calculation of RMSDs using a quaternion-based characteristic polynomial

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

PDB file parser and structure class implemented in Python

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

VMD: visual molecular dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

Simulaid: A simulation facilitator and analysis program

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

Wordom: a program for efficient analysis of molecular dynamics simulations.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3144279

29 October 2018

Identifiers

DOI

10.1002/JCC.21787

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journals/jcc/Michaud-AgrawalDWB11

29 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

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29 July 2017

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