Protein Ligand Docking Program In Python
2
4
Entering edit mode
9.2 years ago
Pappu ★ 1.9k

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.

docking python biopython • 6.5k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
9.2 years ago
João Rodrigues ★ 2.5k

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

ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
3
Entering edit mode
9.2 years ago
Jan Kosinski ★ 1.6k

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2347 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6