Dock 3.8

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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

Using BLASTERMASTER

Using DOCKOPT

Docking with SLURM

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