Docking and Virtual Screening
FRED - Fast Exhaustive Docking
Within a given, but practical, resolution FRED performs a systematic and non-stochastic examination of all possible protein-ligand poses, filters for shape complementarity and chemical feature alignment before selecting and optimizing poses using the Chemgauss4 scoring function [1,2,3,4]. It comes with a powerful GUI for preparing the active site and adding custom restraints. It also provides a detailed scoring analysis that uses our Grapheme toolkit. In one example, Brus et al used FRED to discover a validated 2.7nM inhibitor of BChE, an Alzheimer's target . The authors describe FRED as "by far the fastest docking tool and thus particularly suitable for ultrahigh-throughput docking".
Especially useful when you possess information solely from the apo-protein structure.
HYBRID - Ligand guided docking
HYBRID uses bound ligand information to improve virtual screening performance, e.g. as POSIT improves poses HYBRID improves enrichment. Like FRED, HYBRID performs a systematic, exhaustive, non-stochastic examination of poses within the protein active site; however, HYBRID reduces this search space based on shape and chemical complementarity to the bound ligand. This ligand-guided docking provides equivalent or better enrichment when compared to most docking procedures [1,2].
Highly valuable when you have information from the holo-protein structure.
For more detailed information on OEDocking, check out the link below: