Stefano Forli
           Olson Molecular Graphics Laboratory
           Dept. Molecular Biology,  MB-5
           The Scripps Research Institute
           10550  North Torrey Pines Road
           La Jolla,  CA 92037-1000,  USA.


[24 Feb 2010]  How to dock flexible rings with AutoDock and live happy
A tutorial for docking flexible rings using AutoDock is available here
The feature is now officially supported in AutoDock 4.2 and allows to dock macrocyclic structures as completely flexible entities.

small water molecule made with PMV


[Coming soon] My PMV/ADT gallery

Some pictures created with PMV, a  multi-purpose visualization  software developed at the MGL. "Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum."

small water molecule made with PMV


[Coming soon] AutoDock | Raccoon

Raccoon is a simple Python/Tk interface I wrote for preparing virtual screenings for AutoDock. Raccoon can convert all file formats supported by AutoDockTools (i.e. PDB, Mol2, PDBQT), and can split automatically multi-structure Mol2 files. For multi-Mol2 files the ZINC codes from the ZINC database are supported (the file names will be the ZINC code). Ligands can also be filtered using a simple set of properties (HB count, number of atoms, MW...). Raccoon can process multiple ligands versus multiple protein structures (for example in the context of a Relaxed Complex simulation).

The Secret Life of A Water Molecule

Comment/suggestions are welcome
scripps .edu


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