Monday, 4 April 2011

PyRx - AutoDocking made simple

I recently presented an AutoDock tutorial at the EBI based around PyRx 0.8, an impressive GUI for AutoDock and Vina by Sargis Dallakyan. It worked out very well, and a big thanks to James Watson from the EBI who helped install all the software. While PyRx still has a few rough edges, it is an order of magnitude easier to use than the existing AutoDock GUI AutoDockTools (although the latter allows more fine-grained control).

We followed the 2010 PyRx tutorial (PyRx2010_rvsnALP_7122010.pdf) available from http://pyrx.scripps.edu/SI/2010/. You will also need the 3D.sdf from that location. You may also want to download sample.tar.gz.

The following notes describe how to get everything set up on Windows:
(1) Download AutoDock 4.2. When installing, install to "C:\Program Files (x86)\AutoDock" not C:\Windows\system32 as suggested.
(2) Download and install PyRx 0.8. This installs to "C:\Program Files (x86)\PyRx".
(3) Replace the appropriate file in "C:\Program Files (x86)\PyRx\Lib\site-packages\PyRx" with importWizard.py, dbPlot.py and autodockNavigator.py.
(4) Have everyone start PyRx (there should be a shortcut on the desktop, else run PyRx.bat) and under Edit/Preferences set the location of AutoDock to "C:\Program Files (x86)\AutoDock\autodock.exe" (they can just browse to the folder and file), and similarly for AutoGrid. If they did this properly, the "Local" radiobutton in the bottom of the AutoDock Wizard tab should be available. They should choose this during the docking.

It should then be possible to work through the tutorial without problems. The tutorial involves docking a single molecule with AutoDock, then running a virtual screen with Vina (I recommend only choosing 5 molecules unless you have lots of time on your hands).

Note that pdbqt files, configuration files and such are saved into C:\Users\MyName\.mgltools\PyRx, if you want to have a look. You can delete this folder to reset PyRx. And all of this software should work equally well on Mac and Linux, although I haven't tested this.

9 comments:

Sarkis Dallakian said...

Thank you very much Noel! PyRx owes a great deal to Open Babel and other open-source programs including AutoDock 4.2 and Vina.

Many Medicinal Chemists are overwhelmed with a rather high barrier of entry into docking and virtual screening. A recent article on Cheminformatic Tools for Medicinal Chemists puts virtual screening under Unknown Unknowns
and in the domain of the expert computational chemist.

I hope that tools like PyRx would lower barriers of entry for medicinal chemists and make virtual screening useful cheminformatic tool in practice.

Cheers!

sah said...

Hi Noel
I did exactly like you mentioned in the blog for installing Pyrx (0.8) in windows xp.
But i am getting error as below:


Error running "C:\Program Files x(86)\Pyrx\vina.exe" --config conf.txt --ligand..\..\Ligands\test.pdbqt


Stderr" 'C:\Program' is not recognized as an internal or external command,operable program or batch file

Any help is greatly appreciated.

baoilleach said...

You should contact PyRx for help...

raman sethi said...

I want to ask the maximum size of the protein molecule (amino acid residues)that can be docked using PyRx?

Noel O'Boyle said...

You should contact PyRx for help...

raman sethi said...

I could not find any e-mail address to contact them..can you provide me the e-mail address to which i should contact?

Sarkis Dallakian said...

I don't know what is the maximum size of the protein molecule that that can be docked using PyRx, since I didn't hit that limit. With 64-bit version of AutoDock, you are practically limited by how much RAM you can afford.

Please visit http://pyrx.sourceforge.net and click on Support This Project on top left, if you need email support.

pushpendra singh said...

hi Sir, i have a problem in i workspace tarball, how can prepare this file,
i have sdf compound library and receptor protein molecule, i want to do virtual screening of ligands molecules.

Nutan Prakash said...

Dear Sir!
I am using the AutoDock Vina in PyRx 0.7.
Is it possible to get the protein-ligand complex after docking, so that i can proceed for the molecular dynamic simulation of the same.