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Protocols

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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Versioning


No version available

Documentation


Maintainers


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

Publication for MDAnalysis

MDAnalysis citations

 (65)
call_split

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
call_split See protocol

[…] nd 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. […]

library_books

Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations

2018
PLoS Comput Biol
PMCID: 5919694
PMID: 29659571
DOI: 10.1371/journal.pcbi.1006103

[…] Unless stated otherwise, analyses of MD trajectories are performed using Python 2.7 and the MDAnalysis module (version 0.15.0) []. Matplotlib is used for plotting data []. VMD is used for visualization of trajectories and production of structural figures [–]. For each substrate state, a sing […]

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. This ide […]

library_books

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function

2018
Sci Rep
PMCID: 5813003
PMID: 29445244
DOI: 10.1038/s41598-018-21357-2

[…] idues. For the permeability calculation we for practical purposes used the center of geometry instead of the COM.Pore radii were calculated using HOLE v.2.2.004.Hydrogen bonds were detected using the MDAnalysis hydrogen bond library, applying a donor-acceptor atom distance cutoff 3.5 Å and a donor-hydrogen-acceptor cutoff angle of 150° (where 180° is linear).The osmotic permeability, pf was calcul […]

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

[…] Visualization was done using VMD, and analysis was done using MDAnalysis. […]

call_split

Solvation dynamics in polar solvents and imidazolium ionic liquids: failure of linear response approximations† †Electronic supplementary information (ESI) available: Higher order and partial correlation functions, corrections to Gaussian statistics and structure analysis for all systems. See DOI: 10.1039/c7cp07052g

2018
Phys Chem Chem Phys
PMCID: 5815284
PMID: 29400383
DOI: 10.1039/c7cp07052g
call_split See protocol

[…] of starting configurations. To the best of our knowledge, no simulation study of the Stokes shift exists on such a large scale. The resulting trajectories were analyzed via a python program based on MDAnalysis. 95% confidence intervals are given, where appropriate, as where x is the average of the property of interest, t the Student t factor, s the standard deviation and n the number of independ […]

Citations

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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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