Understanding MakeDOCK, which automates sphere and grid generation

What is MakeDOCK?

• MakeDOCK automates the process of sphere and grid generation for a target.

Input files to MakeDOCK

• The following files are required to specify the target for MakeDOCK:

1. rec.pdb: Prepared receptor file
2. xtal-lig.mol2 (or .pdb): Ligand specification file

Receptor Preparation

To prepare a typical pdb structure for use as the receptor in MakeDOCK, perform the following steps:

1. Remove solvent (i.e. crystallographic waters)
2. Remove other non-essential hetero-atoms (everything but perhaps a co-factor essential for ligand binding)
3. Remove the ligand itself
4. Delete all hydrogens
5. Renumber residues to be monotonically increasing
6. Save as rec.pdb

Ligand Preparation

To prepare the ligand specification, reload the original pdb structure and perform the following steps:

1. Delete everything BUT the ligand atoms
2. Add hydrogens and charges (optional but advised)
3. Save as xtal-lig.mol2