Virtual Screening Protocol
In this document, the current Rizzo group protocol will be described in detail. This protocol has be through successive iterations and has be used to select compounds for Flu and HIVgp41 (n=112).
Contents
ZINC Database
ZINC is a free, online database of commercially-available compounds. In June 2009, the "big" vendor libraries at a pH of 7 were downloaded and processed into chunks of approximately 100,000 molecules each. The ZINC molecules come with AMSOL charges already determined.
These chunks are then processed through MOE and sorted by rotatable bonds in ascending order. These processed chunks are available on BG, path=~pholden/RCR/projects_ZINC8/ZINC8, or on ringo, path=/media/sdb1/pholden/ZINC8.descending.rot.bonds. The lab is currently using the ChemDiv library for its virtual screen.
Downloading and Preparation of Receptor
Preparation of Reference Molecule for Footprint Rescoring
DOCKing
The version of DOCK currently being used for virtual screening is dock6_09-09-08.footprint.
