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.
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Pappu
PTools is Python/C++ and open-source. Sounds like a good place to start.
You can take a look at AutoDockTools/AutoDock as well, but that's more of an application that a library.
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
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.
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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