v2.1

Updated Zenodo badge to point to v2.0 of the tutorial.

Added updated citations and DOI (for PSA paper in PLOS Computational Biology):

Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1004568 (also: arXiv:1505.04807 [q-bio.QM])

v2.0

Code and data that supplement the revised PSA paper (provisionally accepted by PLOS Computational Biology). The submitted version of the manuscript is on the arXiv (as version 1; an updated version will be uploaded to the arXiv to reflect revisions made for publication in PLOS Computational Biology):

Sean L. Seyler, Avishek Kumar, Michael F. Thorpe, Oliver Beckstein. Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways. arXiv:1505.04807 [q-bio.QM]

Changes include:

• Compatibility with new API for MDAnalysis release 0.11.0 and the PSAnalysis module in 0.11.1(-dev)
• Trajectory data updated to match data in the accept PSA manuscript, including:
  • 3 restrained TMD simulations (from NAMD) with slow pulling
  • 3 restrained TMD simulations (from NAMD) with fast pulling
• A new Hausdorff pair analysis script demonstrating Hausdorff pair and nearest neighbor calculations (for each pair of paths among a set of paths)
• A new PairID convenience class for accessing PSA data by method name
• Updated psa_short.py and psa_full.py scripts which now
  • generate both Hausdorff and Frechet distance matrices
  • produce annotated heat maps that display the numerical distances
• A new PairID convenience class for accessing PSA data by method name
• A Jupyter notebook for demonstrating how to use PairID, as well as versions of the (above) python scripts to:
  • perform interactive analysis
  • demonstrate the use of PairID to access data

v1.0

Code and data that supplement the paper

Sean L. Seyler, Avishek Kumar, Michael F. Thorpe, Oliver Beckstein. Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways. arXiv:1505.04807 [q-bio.QM]