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README.md

MSMSeeder

Software pipeline used to generate diverse protein structural ensembles, for the purpose of seeding multiple parallel molecular dynamics simulations, and subsequent construction of Markov state models. This branch contains a version of MSMSeeder which runs via the distributed computing framework Spark (https://spark.apache.org/)

Authors

Overview of pipeline

  1. Retrieve protein target sequences and template structures.
  2. Build models by mapping each target sequence onto every available template structure, using Modeller (http://salilab.org/modeller/).
  3. Filter out non-unique models (based on a RMSD cutoff).
  4. Refine models with implicit solvent molecular dynamics simulation.
  5. Refine models with explicit solvent molecular dynamics simulation.
  6. (optional) Package and/or compress the final models, ready for transfer or for set-up on other platforms such as Folding@Home.

Manifest

scripts/ - Python wrapper scripts which accept parameters from the command-line or project metadata file

MSMSeeder/ - main code; can be used as a standalone Python library package

tests/ - to test whether the code is working correctly, run nosetests from this top-level directory

Installation

git clone https://github.com/choderalab/msmseeder.git
cd msmseeder
python setup.py install

Dependencies

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