MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
University of Manchester · Université de Picardie Jules Verne · +10 more institutions
Abstract
MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output trajectories in their own formats so that the development of new trajectory analysis algorithms is confined to specific user communities and widespread adoption and further development is delayed. MDAnalysis addresses this problem by abstracting access to the raw simulation data…
Citation impact
- FWCI
- 24.72
- Percentile
- 100%
- References
- 48
Authors
11- RGRichard GowersCorresponding
University of Manchester, Université de Picardie Jules Verne, Arizona State University, University of Edinburgh
- MLMax Linke
University of Manchester, Max Planck Institute of Biophysics, Université de Picardie Jules Verne, Arizona State University, University of Edinburgh
- JBJonathan Barnoud
Biotechnology Institute, University of Groningen
- TRTyler Reddy
University of Manchester, University of Oxford
- MNManuel N. Melo
University of Groningen, University of Manchester, Universidade Nova de Lisboa
Topics & keywords
- Python (programming language)
- Computer science
- Modular design
- Interoperability
- Scripting language
- Visualization
- User interface
- USable
Funding
- ASArizona State University
- WTWellcome Trust
- LTLeverhulme Trust
- PFPartnership for Advanced Computing in Europe AISBL
- NONederlandse Organisatie voor Wetenschappelijk OnderzoekAward: 722.013.010
- MMax-Planck-Gesellschaft
- CICanadian Institutes of Health Research
- BABiotechnology and Biological Sciences Research CouncilAward: BB/J014478/1