Dock 3.8 - Revision history

Wtitulaer at 15:57, 28 August 2024

2024-08-28T15:57:04Z

← Older revision		Revision as of 15:57, 28 August 2024
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	==Initializing DOCK on cn142==		==Initializing DOCK on cn142==
	In order to run DOCK 3.8 programs, the correct environment first needs to be loaded. '''EDIT: A more sophisticated login script will appear soon (hopefully). For now do the actions below'''.		In order to run DOCK 3.8 programs, the correct environment first needs to be loaded. '''EDIT: A more sophisticated login script will appear soon (hopefully). For now do the actions below'''.
	~~Execute the~~		Ssh into cn142 then:

	<pre>		<pre>
	#!/~~bin~~/~~bash~~		source /opt/molmech/login_molmech.sh
	~~echo "This is a script"~~		module load poetry
	cd /~~path~~/to/~~directory~~		cd /opt/molmech/modules$ cd /opt/molmech/DOCK38/DOCK_Release_Apr_21_2023/pydock3/
	~~ls -l~~		poetry shell
	</pre>		</pre>
	==Using BLASTERMASTER==		==Using BLASTERMASTER==

Wtitulaer at 15:55, 28 August 2024

2024-08-28T15:55:23Z

← Older revision		Revision as of 15:55, 28 August 2024
Line 13:		Line 13:
	DOCK operates by first generating spheres based on a protein-ligand complex and then docking a pre-generated conformer library on those. It calls the program BLASTERMASTER for this, for which you want to		DOCK operates by first generating spheres based on a protein-ligand complex and then docking a pre-generated conformer library on those. It calls the program BLASTERMASTER for this, for which you want to

			==Initializing DOCK on cn142==
			In order to run DOCK 3.8 programs, the correct environment first needs to be loaded. '''EDIT: A more sophisticated login script will appear soon (hopefully). For now do the actions below'''.
			Execute the

			<pre>
			#!/bin/bash
			echo "This is a script"
			cd /path/to/directory
			ls -l
			</pre>
	==Using BLASTERMASTER==		==Using BLASTERMASTER==

Wtitulaer: Created page with "DOCK is a molecular docking software developed at UCSF for large to ultra large-scale virtual screening. The most recent comprehensive guide on DOCK 3.8 can be found [https://..."

2024-08-28T15:43:13Z

Created page with "DOCK is a molecular docking software developed at UCSF for large to ultra large-scale virtual screening. The most recent comprehensive guide on DOCK 3.8 can be found [https://..."

New page

DOCK is a molecular docking software developed at UCSF for large to ultra large-scale virtual screening. The most recent comprehensive guide on DOCK 3.8 can be found [https://doi.org/10.1038/s41596-021-00597-z here]. The software can be used by academics upon requesting a license and currently runs on cn142.

==Pros & Cons of DOCK as docking software==
* '''Pro''' DOCK is generally a lot faster than other docking software available.
* '''Pro''' DOCK generally produces accurate poses if sampling is increased
* '''Pro''' Tuning of parameters can be done through manipulating the spheres and scoring functions, allowing for better optimization.
* '''Con''' DOCK doesn't generates conformers of ligands on-the-fly and requires additional software to do this.
* '''Con''' DOCK doesn't have very clear documentation, requiring more hands-on programming knowledge/experience to use.

Basically, DOCK is the go-to virtual screening software on our cluster.
=How to use=
==Protein-ligand complex files to generate==
DOCK operates by first generating spheres based on a protein-ligand complex and then docking a pre-generated conformer library on those. It calls the program BLASTERMASTER for this, for which you want to

==Using BLASTERMASTER==

==Using DOCKOPT==

==Docking with SLURM==