Galaxy | Tool Preview

rDock cavity definition (version 2013.1-0+galaxy0)
Select a receptor (Mol2 format).
Single ligand in Mol or SDF format
Mapper radius of large sphere in angstroms; rDock will search for cavities to the small sphere but not to the large sphere
Mapper radius of small sphere in angstroms; rDock will search for cavities accessible to the small sphere but not to the large sphere
Mapper minimum volume in cubic angstroms. rDock will ignore cavities which are smaller than this value
Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rDock will temporarily increase the radius of receptor atoms by this amount
Grid resolution for mapping in angstroms
Cavity weight

This tool generates the cavity definition for rDock docking (the receptor.as file) using the rbcavity program. See http://rdock.sourceforge.net/ for more details about rDock and associated programs. Only a subset of the parameters are currently exposed. Read the rDock docs for a full understanding.


Inputs

  1. The protein receptor to dock into as a file in Mol2 format.
  2. A reference ligand used to define the location of the active site in Molfile or SDF format.
  3. Various parameters for the mapper and cavity generation. Sensible defaults are provided for all.

Outputs

An active site definition binary file (receptor.as) that is needed by the rDock docking program to guide the docking.