Ucsfdock

ucsfdock is a Python package wrapping the DOCK program that provides tools to help standardize and automate the computational methods employed in molecular docking.

Programs:

• blastermaster: given receptor and ligand, generate a specific docking configuration
• dockmaster: evaluate many different docking configurations in parallel using a provided job scheduler (e.g. Slurm)

Installation

1. TODO

Quickstart

blastermaster

blastermaster configure

First you need to create the directory for your blastermaster job. To do so, simply type

blastermaster configure

By default, the job directory is named blastermaster_job. To specify a different name, type

blastermaster configure <JOB_DIR_NAME>

The job directory contains two sub-directories:

1. working: blaster files, sub-directories for individual subroutines
2. dockfiles: DOCK parameter files & INDOCK file

If your current working directory contains any of the following files

• rec.pdb
• xtal-lig.pdb
• rec.crg.pdb
• reduce_wwPDB_het_dict.txt
• filt.params
• radii
• amb.crg.oxt
• vdw.siz
• delphi.def
• vdw.parms.amb.mindock
• prot.table.ambcrg.ambH

then they will be automatically copied into the working directory within the generated blastermaster job directory. If you would like to use

blastermaster run

Now

dockamster

1. TODO