Computational Methods in Drug Discovery

Lab for Molecular Design & Pharmaceutical Biophysics
Institute of Pharmaceutical Sciences in the group of

This repository contains the work of my internship in 2017 as part of my undergraduate studies in Bioinformatics at the University of Tübingen, Germany.

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Content

The script is a Python script written for the PyMOL by Schrödinger program. The script expects 2 files of the type mol2, a halogen and a nitrogen as input. In the first step, these two molecules are rotated and aligned around the axes x, y and z by selecting individual atoms. A copy of the halogen is then created and a grid is later created from this copy. The halogen is copied again several times and placed at the grid points. These grid points can be entered manually or generated randomly.

Then the coordinates and points of the halogen copies are saved in a .mol2 file. For the randomized grid generation, a statistical evaluation of the angles of rotation around the axes is also shown in a plot in order to see the distribution

PyMOL

https://pymol.org/2/
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.

Input Parameters

Filename1 = "/Mol2/file1.mol2" 
Filename2 = "/Mol2/file2.mol2"
pathToSave = "/Results"
fileType  = "mol2"

Included packages

from pymol import cmd
from pymol import math
import numpy
import random
import  matplotlib
import  matplotlib . pyplot  as  plt