Basic usage

Once installed, the CryptoSite protocol can be run by means of a command line tool (cryptosite). Each component of the protocol is also a Python package, which can be called directly from other Python software (via import cryptosite).


Running the basic protocol consists of these steps:

  1. Create a set of input files specifying the structure to probe, and basic CryptoSite parameters.
  2. Run cryptosite setup to calculate structural features and prepare input files for AllosMod.
  3. Run AllosMod given the set of input files.
  4. Calculate additional features using the AllosMod output (cryptosite soap, cryptosite pockets, cryptosite am_bmi, cryptosite analysis).
  5. Gather together all features into a single file (cryptosite gather).
  6. Predict cryptic binding sites with an SVM using the complete set of features as input (cryptosite predict).
  7. Optionally visualize the results in Chimera (cryptosite chimera).