Virtual Screening Protocol

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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).

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


Minimization of Poses

Pose Rescoring using Molecular Footprints

Clustering using MOE

Compound Selection