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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.


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/


See: blastermaster (pydock3 script).


See: dockopt (pydock3 script).