MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations

By Naveen Michaud-Agrawal, Elizabeth J. Denning, T. Woolf, O. Beckstein. Journal of Computational Chemistry, 2011

3,756 citations recorded by the source corpus.

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

Subfields: Atomic and Molecular Physics, and Optics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9a0557d4cd6506ff5903670f75bb6df7fbed58e4

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In Atomic and Molecular Physics, and Optics

Jeffrey J. Gray

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane. (2020, methodology): “MDAnalysis (42) was used to extract water-density information from each bilayer simulation.”
Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification (2017, background): “where xi is the distance between the Cα atom of the snapshots at a given time and the Cα atom of the ith residue of the reference structures (57).”
Ins and outs of AlphaFold2 transmembrane protein structure predictions (2022, methodology): “MDAnalysis [56] and NumPy [57] Python packages were used for calculation of mean pLDDT values and hydrophobic membrane thickness.”
Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges (2013, methodology): “Concerning analysis facilities (including atom selection and scripting) we intend to link UnityMol to existing frameworks such as for example MDAnalysis [36].”