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Docking-based virtual screening of enzymes active sites.

Perl scripts and data to performa a virtual screening of a library of enzyme active sites using a given substrate. Coinceived for a High Performance Computer (HPC) cluster

Getting Started

Prerequisites

AutoDock, AutoGrid >=4.2.6

Mgltools >=1.5.6

Perl, Python, linux

Example

Screen a library of enzyme active sites with a particular substrate

./procedure_reverse_docking_p.pl rd_conf_HTML_PLP.txt

See rd_conf_HTML_PLP.txt for required files

A list of pdb entries with x y z coordinates to center the grid can be obtained with the following utility:

./Utility_scripts/procedure_get_coord_from_resn.pl -a NZ Human/Human_Orf_pred.resn Human/pdb

The command will extract coordinates from the pdb files stored in the Huma/pdb directory.

Pdb_id, chain, and residue number are specified in the input file; the -a option specifies the particular atom (default CA).

See Human_Orf_pred.resn for input file specs