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.

Scripts: - 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

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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 the job directory name, you can do

blastermaster configure <JOB_DIR_NAME>

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

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