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Volume 109, Issue 8, Pages (October 2015)

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1 Volume 109, Issue 8, Pages 1528-1532 (October 2015)
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories  Robert T. McGibbon, Kyle A. Beauchamp, Matthew P. Harrigan, Christoph Klein, Jason M. Swails, Carlos X. Hernández, Christian R. Schwantes, Lee-Ping Wang, Thomas J. Lane, Vijay S. Pande  Biophysical Journal  Volume 109, Issue 8, Pages (October 2015) DOI: /j.bpj Copyright © 2015 Biophysical Society Terms and Conditions

2 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). Biophysical Journal  , DOI: ( /j.bpj ) Copyright © 2015 Biophysical Society Terms and Conditions

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. Biophysical Journal  , DOI: ( /j.bpj ) Copyright © 2015 Biophysical Society Terms and Conditions

4 Figure 3 Demonstration of PCA with MDTraj, scikit-learn, and MATPLOTLIB. To see this figure in color, go online. Biophysical Journal  , DOI: ( /j.bpj ) Copyright © 2015 Biophysical Society Terms and Conditions

5 Figure 4 Demonstration of solvent-accessible surface area calculation done in parallel with MDTraj and IPython. To see this figure in color, go online. Biophysical Journal  , DOI: ( /j.bpj ) Copyright © 2015 Biophysical Society Terms and Conditions

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