Author: Ragul Gowthaman (g.ragul at gmail.com)
This document was last updated May 28, 2015, by Ragul Gowthaman.
The corresponding principal investigator is John Karanicolas (firstname.lastname@example.org).
This application takes in a protein and ligand PDB files and outputs the "theta-lig" value, which is the fraction of ligand that is exposed to the solvent in the complex. See the referred paper for more details.
Gowthaman R, Deeds EJ, and Karanicolas J. (2013) The structural properties of non-traditional drug targets present new challenges for virtual screening. J. Chem. Inf. Model, 53(8), p. 2073-81.
~/Rosetta/main/source/bin/theta_lig.macosgccrelease -input_protein_ligand_complex protein_ligand_complex.pdb -input_protein protein.pdb -input_ligand LIGAND_0001.pdb -extra_res_fa LIGAND.params
General Rosetta Options -database Path to rosetta databases
-input_protein_ligand_complex : PDB file of protein-ligand complex
-input_protein : PDB file of bound protein
-input_ligand : PDB file of bound ligand
To generate parameter file for the ligand one can use the 'molfile_to_params.py' script.
Rosetta/main/source/scripts/python/public/molfile_to_params.py -p LIGAND LIGAND.mol2