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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
Open accessAbstract
MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance‐critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix‐based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011
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VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535
Cited by
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
AI-based structure prediction empowers integrative structural analysis of human nuclear pores
Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., Buczak, K., Schmidt, F. H., Margiotta, E., Mackmull, M.-T., et al. (2022) · Science · doi:10.1126/science.abm9506 · Cited by 355
Fong, K. D., Self, J., Diederichsen, K. M., Wood, B. M., McCloskey, B. D., & Persson, K. A. (2019) · ACS Central Science · doi:10.1021/acscentsci.9b00406 · Cited by 239
Hsu, P., Bruininks, B. M. H., Jefferies, D., Cesar Telles de Souza, P., Lee, J., Patel, D. S., Marrink, S. J., Qi, Y., Khalid, S., & Im, W. (2017) · Journal of Computational Chemistry · doi:10.1002/jcc.24895 · Cited by 202
Water-induced correlation between single ions imaged at the solid–liquid interface
Ricci, M., Spijker, P., & Voïtchovsky, K. (2014) · Nature Communications · doi:10.1038/ncomms5400 · Cited by 188
Metadata
- Authors
- Michaud‐Agrawal, N., Denning, E. J., Woolf, T. B., & Beckstein, O.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2011-04-15
- Volume
- 32
- Issue
- 10
- Pages
- 2319-2327
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2170711116
- Cited by
- 4,486
- References
- 2
- FWCI
- 11.99
- Type
- journal article
- Language
- en
- Open access
- green
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