Ligand Score

To score ligand poses, use the ligand_score command line tool.

Two different scoring files are provided:

protein_ligand_pose_score.lib for use when one wants to find the most near-native poses of a ligand from many geometry decoys of the same ligand
protein_ligand_rank_score.lib for use when screening a compound database against a single protein to choose putative binders.

The rank score is used by default.

They are both located in the IMP.atom data directory. This directory is available within IMP python scripts via the IMP::atom::get_data_path() function. From the command line, the files can be found at build/data/atom if IMP is not installed or something like /usr/share/imp/data/atom if it is installed.

Info

Author(s): Hao Fan, Daniel Russel

Maintainer: benmwebb

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

Hao Fan, Dina Schneidmann, John Irwin, G Dong, Brian Shoichet, Andrej Sali. “Statistical Potential for Modeling and Ranking Protein-Ligand Interactions”, J Chem Inf Model 51, 3078-3092, 2011.