Question: Protein Ligand Docking Program In Python
3
gravatar for Pappu
7.8 years ago by
Pappu1.9k
Pappu1.9k wrote:

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.

python biopython docking • 5.2k views
ADD COMMENTlink written 7.8 years ago by Pappu1.9k
3
gravatar for João Rodrigues
7.8 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

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

ADD COMMENTlink written 7.8 years ago by João Rodrigues2.5k
1

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

ADD REPLYlink written 7.8 years ago by Pappu1.9k

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

ADD REPLYlink written 7.8 years ago by Michael Schubert6.9k
3
gravatar for Jan Kosinski
7.8 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

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 COMMENTlink written 7.8 years ago by Jan Kosinski1.6k

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

ADD REPLYlink written 7.8 years ago by Pappu1.9k

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 REPLYlink written 7.8 years ago by Jan Kosinski1.6k
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