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pydock3 is a Python package wrapping the DOCK Fortran program that provides tools to help standardize and automate the computational methods employed in molecular docking. It is a natural successor to DOCK Blaster, originally published in 2009, and, part of the DOCK 3.7 release in 2012.

Scripts included in pydock3:

  • dockopt: generate many different docking configurations, perform retrospective docking on them in parallel using a specified job scheduler (e.g. Slurm), and analyze the results.
  • blastermaster: generate a specific docking configuration for a given receptor and ligand, intended for use by experts who wish to tune the docking model themselves. This is a direct successor of from DOCK 3.7.

A docking configuration is a unique set of (1) DOCK parameter files (e.g., matching_spheres.sph), (2) an INDOCK file, and (3) a DOCK executable.


See: DOCK 3.8:How to install pydock3.



See: blastermaster (pydock3 script).


See: dockopt (pydock3 script).

Note for UCSF Shoichet Lab members

pydock3 is already installed on the following clusters. You can source the provided Python environment scripts to expose the pydock3 executable:


 source /wynton/group/bks/soft/python_envs/


Only nodes other than gimel itself are supported, e.g., gimel5.

ssh gimel5
source /nfs/soft/ian/