Dock 3.8

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 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

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

#!/bin/bash
echo "This is a script"
cd /path/to/directory
ls -l