Package selection

To define the type of simulation to run, a package needs to be selected in the input.yaml. There are several packages available in the Platform. Some of them can be activated by setting specific parameters to True. They are listed below:

Local explorations

• induced_fit_fast: fast induced-fit docking protocol. More information here.

• induced_fit_long: more expensive induced-fit docking protocol. More information here.

• rescoring: local conformation refinement. More information here.

Global explorations

• out_in: ligand migration from the bulk of solvent to a protein cavity. More information here.

• in_out: ligand migration from a protein cavity to the bulk of solvent. More information here.

• site_finder: global search of ligand binding sites. More information here.

Other packages can be activated when specific parameters are set, like:

• fragPELE: our fragment growing protocol has its own parameters. More information here.

• sidechainPerturbation: when covalent_residue is set, the side chain perturbation algorithm will run to perturb covalently bound non standard residues. More information here.