This script calculates the necessary descriptors for calculating the druggability of a protein pocket using the PockDrug function. Also, it creates the matrix file used in PockDrug.R* to solve the druggability of a portein pocket.
*PockDrug druggability function was published in "A., Regad, L., Xhaard, H., Petitjean, M., & Camproux, A. C. (2015). PockDrug: a model for predicting pocket druggability that overcomes pocket estimation uncertainties. Journal of chemical information and modeling, 55(4), 882-895." and the software can be found in its Supporting information.
If you use this script, please cite the website https://github.com/rodriguez-salarichs/PockDrug_descriptors_calculations/
######################################################################################### IMPORTANT: This script uses RADI to calculate the geometric descriptors (RADIUS_CYLINDER, SMALLEST_SIZE, VOLUME_HULL, RADIUS_HULL, DIAMETER_HULL and SURFACE_HULL) #########################################################################################
script.sh [options] -i file.pdb -f RADI -n NAME
options:
-i Input file (FOrmat: PDB)
-f address of RADI executable
-n Name of pocket (Default: 1)
-h Print this help
version:
version : 1.0
author : Dr. Javier Rodriguez-Salarichs