DOCK 3.8

DOCK 3.8 has been the primary version of DOCK 3 since January 2021.

DOCK 3.8 is now organized in three separate github repos.

* Dock3 - the fortran source code 
* PyDOCK3 - the scripts and executables to run docking
* LigDOCK3 - the ligand building scripts used by ZINC-22. 

DOCK 3.8 has been extensively reorganized from DOCK 3.7.

How to get DOCK 3.8. Use the DOCK license server dock.compbio.ucsf.edu. If you are a developer, fork the relevant repo.

How to install DOCK 3.8

How to dock in DOCK3.8

Docking Analysis in DOCK3.8

how to build libraries for DOCK 3.8

Programming DOCK 3.8

DOCK 3.8.5 is the current production version of DOCK 3, as of Sept 1, 2022.

Availability

DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS and OCI as a docker container. The software has never been easier to install (low bar!). It should be runnable on any modern HPC platform. We recommend using an OS were python 3.8 or later is installed by default, however, you should be able to install python 3.8 or later on older equipment.

General Use

Mechanically, docking has the following steps.

• prepare gridfiles (dockfiles)
• select database subset to run
• move all files to the target platform
• run docking at scale
• merge the results (top_poses.py)
• move results back to your server.
• process the results (interaction fingerprint, strain filter, clustering, manual review)
• final re-extract of top poses for hit picking party.
• archive the results.

Step by Step instructions

During development, this was the script we used to explain how to dock: How to dock in DOCK3.8