Docking A Small Series Of Compunds Against A Set Of Proteins Using Perl

Question

[Saad Khan]

Hi all I have a small series of compound that I got from a friend of mine for docking against a set of proteins from PDB. As I need to do blind docking on all of the proteins and the procedure happens to be redundant, I was wondering if it can be done pro-grammatically using perl preferably. I also did not have much success with energy minimization using chemical tollboxes like MMTK and openbabel from perl.

[Saad Khan]

Thanks WoA I am using autodock 4 for docking although it has certain python scripts that i can use from perl to automate the docking. But predocking there are certain tasks like energy minimization of the ligand compund that also need to be done. I have tried with MMTK which is almost impossible to install in Ubuntu 9.10. And due to my lack of knowledge in python i am unable to use openbabel library.Please suggest a perlish alternative thanks.

[Vladimir Chupakhin]

What is the perl motivation?

Answer 1

[Michael Schubert]

Do yourself a favour and install PyMOL+AutoDock Vina+this PyMOL plugin (GUI-only solution, no Python required) instead of using Perl to call Python to call AutoDock ;-)

It supports virtual screening of multiple proteins and compounds, plus it has a video tutorial.

That would also have the advantage that you don't have to care too much about:

• adding hydrogens to receptor and ligand
• adding charges to receptor and ligand
• generate different poses of compound library
• setting up the force field
• loop through all possible combinations
• score them
• ...

To sum up, there's a lot to look after! I would recommend not trying to write automation scripts before you know more about the process you're trying to automate and have to apply it on a scale where there are no convenient alternatives.

[Saad Khan]

Thanks a lot Michael

Answer 2

[Woa]

What I could understand from your question that you would like to automate the docking process through Perl. I don't know any dedicated perl module available for this kind of job, or any docking program written in Perl for that matter. However. most docking program suites come with their own scripting language. I can remember FlexX, ICMDock and (Yasara)Autodock have scripting features for batch jobs which at one time I used quite a lot.

I never used the program SLIDE (which has some Perl stuff inside), but now it has got a Pymol plugin and you might be able to run batch jobs using Pymol's rich features.