Galaxy |

rxDock cavity definition (version 2013.1.1_148c5bd1+galaxy0)

Receptor:

Select a receptor (Mol2 format).

Reference ligand:

Single ligand in Mol or SDF format

Mapper sphere radius:

Mapper radius of large sphere in angstroms; rxDock will search for cavities to the small sphere but not to the large sphere

Mapper small sphere radius:

Mapper radius of small sphere in angstroms; rxDock will search for cavities accessible to the small sphere but not to the large sphere

Mapper minimum volume:

Mapper minimum volume in cubic angstroms. rxDock will ignore cavities which are smaller than this value

Mapper volume increment:

Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rxDock will temporarily increase the radius of receptor atoms by this amount

Mapper grid step:

Grid resolution for mapping in angstroms

Cavity weight:

Cavity weight

This tool generates the cavity definition for rxDock docking (the receptor.as file) using the rbcavity program. See https://www.rxdock.org for more details about rxDock and associated programs. Only a subset of the parameters are currently exposed. Read the rxDock docs for a full understanding.

Inputs

The protein receptor to dock into as a file in Mol2 format.
A reference ligand used to define the location of the active site in Molfile or SDF format.
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 rxDock docking program to guide the docking.