Protein Ligand Docking Program In Python

Question

[Pappu]

Please let me know how to make a small molecular docking program in python using external libraries. I want to do it in order to find out how a docking program exactly works.

[Anonymous]

Hi! Obviously it's been a while since you asked this question. Would you by any chance have such a Python program on Molecular Docking? Now I'm looking for this, I'm a total beginner btw

Answer 1

[João Rodrigues]

PTools is Python/C++ and open-source. Sounds like a good place to start.

[Pappu]

PTools is for protein-protein or protin nucleic acid docking. I am looking for small molecule docking program.

[Michael Schubert]

You can take a look at AutoDockTools/AutoDock as well, but that's more of an application that a library.

Answer 2

[Jan Kosinski]

You should definitely play with PyRosetta

First get familiar how to use PyRosetta in general.

Then for small ligand docking, a good start will be ligand_interface.py script at:

http://www.pyrosetta.org/scripts#TOC-Sample-Scripts

and info at:

http://www.pyrosetta.org/obtaining-and-preparing-ligand-pdb-files

[Pappu]

Thanks. I am aware of PyRosetta. But I wonder how good it is for protein ligand docking.

[Jan Kosinski]

You have to look at the Rosetta Ligand papers: http://www.ncbi.nlm.nih.gov/pubmed/22183535, http://www.ncbi.nlm.nih.gov/pubmed/19041878, http://www.ncbi.nlm.nih.gov/pubmed/19554568, However, for you, "in order to find out how a docking program exactly works" you don't need the best docking program out there, right? You just need a python package that makes it possible to experiment with conformational sampling methods and scoring functions.