Automated Database Preparation

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Automated Docking Database Tools

  1. #Automatic Database Generation: You want to generate your own hierarchy databases as ligand inputs to DOCK 3.5
  2. #Automatic Decoy Generation: You want to generate DUD style decoys from your set of input ligands

Automatic Database Generation

Simple Database Generation

For automated database generation on small input files (say < 5000).

mkdir new_dir_name
cd new_dir_name
dbgen.csh INPUT
< or >
dbgen.csh INPUT [PROTONATION]

Making the new directory is a good idea because these scripts generate a LOT of output files. INPUT is a file containing the ligand molecules, either a .smi file containing lines of smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The optional PROTONATION argument can be used to generate databases containing extended protonation states. The available protonation types are as follows: 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"

dbgen.csh is most useful when you want to test out a dockable database without worrying about ZINC. If you like the molecules and decide to add them to ZINC, this should be easy using the output of dbgen.csh. If you want to add the molecules to ZINC from the beginning then use cmdR2.csh.

Section 2

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