Automated Database Preparation

Automatic Database Preparation Overview

• Scenario: You want to generate your own hierarchy databases as ligand inputs to DOCK 3.5
• See XXX if you want to automatically build a dockable database.
• See YYY if you want to automatically generate decoys

Simple Database Generation

dbgen.csh INPUT
< or >
dbgen.csh INPUT PROTONATION

INPUT is a file containing the ligand molecules, either a .smi containing smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The option PROTONATION can be used to generate databases containing extended protonation states. Available PROTONATION types: ref - only the reference protonation" mid - reference plus middle protonation [default]" lo - reference, middle, and lo protonation" hi - reference, middle, and hi protonation" all - all protonation ranges"

Section 2

• bullet3
• bullet4