DOCK3.8:Pydock3: Difference between revisions
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See: [[How to install pydock3]]. | See: [[DOCK 3.8:How to install pydock3]]. | ||
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See: [[dockopt (pydock3 script)]]. | See: [[dockopt (pydock3 script)]]. | ||
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Revision as of 19:46, 12 September 2022
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.
Scripts included in pydock3:
- blastermaster: generate a specific docking configuration for a given receptor and ligand
- 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.
A docking configuration is a unique set of DOCK parameter files (e.g., matching_spheres.sph) and INDOCK parameter values.
Installation
See: DOCK 3.8:How to install pydock3.
Instructions
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:
Wynton
source /wynton/home/irwin/isknight/envs/python3.8.5.sh
Gimel
Only nodes other than gimel itself are supported, e.g., gimel5.
ssh gimel5 source /nfs/soft/ian/python3.8.5.sh
blastermaster
See: blastermaster (pydock3 script).
dockopt
See: dockopt (pydock3 script).