MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories - PubMed (original) (raw)

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Robert T McGibbon et al. Biophys J. 2015.

Abstract

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.

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Figures

Figure 1

The MDTraj atom selection language. Queries can be expressed using standard Python code (line 2), or an intuitive string-based syntax (line 3).

Figure 2

MDTraj’s interactive WebGL-based protein and trajectory viewer. This feature requires a modern WebGL-enabled browser, and the IPython notebook that can be installed with Conda using the command conda install IPython-notebook. To see this figure in color, go online.

Figure 3

Demonstration of PCA with MDTraj, scikit-learn, and MATPLOTLIB. To see this figure in color, go online.

Figure 4

Demonstration of solvent-accessible surface area calculation done in parallel with MDTraj and IPython. To see this figure in color, go online.

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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories - PubMed (original) (raw)