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MDAnalysis specifications

Information


Unique identifier OMICS_18200
Name MDAnalysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Mac OS
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.16.0
Stability Stable
Requirements
Numpy
Maintained Yes

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Maintainers


  • person_outline Oliver Beckstein
  • person_outline Naveen Michaud-Agrawal
  • person_outline Elizabeth Denning
  • person_outline Thomas Woolf

Publication for MDAnalysis

MDAnalysis citations

 (66)
library_books

Clinically relevant mutations in the ABCG2 transporter uncovered by genetic analysis linked to erythrocyte membrane protein expression

2018
Sci Rep
PMCID: 5945641
PMID: 29749379
DOI: 10.1038/s41598-018-25695-z

[…] mutant nbds using gromacs with charmm36m force field,. for simulation details see the supplementary materials. analysis was performed by employing gromacs tools, vmd network wizard plugin, and the mdanalysis python package., the datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request., , boglárka zámbó, zsuzsa […]

library_books

Theoretical principles of transcription factor traffic on folded chromatin

2018
Nat Commun
PMCID: 5928121
PMID: 29712907
DOI: 10.1038/s41467-018-04130-x

[…] threshold, t. note that distances must be calculated taking into account the periodic boundary conditions of the simulation box. all the distance matrices were computed using the python package mdanalysis. for each of the statistically independent snapshots of the system, we evaluated the contact matrix. the final matrix, h, is given by the sum of the contact matrices for each snapshot., […]

library_books

Crystal structure of undecaprenyl pyrophosphate phosphatase and its role in peptidoglycan biosynthesis

2018
Nat Commun
PMCID: 5852022
PMID: 29540682
DOI: 10.1038/s41467-018-03477-5

[…] parameters, with a verlet cutoff scheme to permit gpu calculation of non-bonded contacts. simulations were performed with an integration time step of 2 fs. the mds were analyzed using gromacs tools, mdanalysis and locally written python and perl scripts., homologous sequences were identified in the uniprotkb database, using eight iterations of jackhmmer, with the default search parameters. […]

library_books

Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association

2018
J Chem Theory Comput
PMCID: 5852462
PMID: 29424543
DOI: 10.1021/acs.jctc.7b00983

[…] that f(r) = 0 for large distances, so that the above integral converges, which can be ensured by adding a suitable constant to f(r)., visualization was done using vmd, and analysis was done using mdanalysis., to determine the free energy surface for glycophorin dimerization, we perform umbrella sampling simulations of the dimer along the interhelical drms coordinate as described […]

library_books

Communication between the leaflets of asymmetric membranes revealed from coarse grain molecular dynamics simulations

2018
Sci Rep
PMCID: 5789016
PMID: 29379141
DOI: 10.1038/s41598-018-20227-1

[…] order and thickness maps were generated using tools developed by n. castillo et al.. the partial density map of a patch of a membrane was calculated using an in house script which utilized the mdanalysis, python module. the script was written to mimic the functionality of the gmx density gromacs tool, but could also analyze subsets of a system which do change size over time. the partial […]

library_books

Interactions of 2’ O methyl oligoribonucleotides with the RNA models of the 30S subunit A site

2018
PLoS One
PMCID: 5774723
PMID: 29351348
DOI: 10.1371/journal.pone.0191138

[…] was followed by a 1150 ns production stage for each system., trajectories were analyzed with the mint package [], ptraj module from ambertools 1.5 [] and in-house written python scripts employing mdanalysis library []. the criteria for the presence of hydrogen bonds were: 3.5 å for the maximal acceptor-donor distance and minimal acceptor-hydrogen-donor angle was set to 150 degrees. the base […]


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MDAnalysis institution(s)
Department of Biophysics and of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Pharmaceutical Chemistry, University of Maryland, Baltimore, School of Pharmacy, Baltimore, MD, USA; Department of Biochemistry, University of Oxford, Oxford, UK
MDAnalysis funding source(s)
Supported in part by a grant from the National Institutes of Health (GM064746), the European Union (EDICT Project, grant 201924) and in part by a Junior Research Fellowship at Merton College, Oxford.

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