Friday 7th June, 2013
11:45am to 12:45pm
The theory that similar ligands often bind to the same protein binding site drives much of the utility of ligand-based virtual screening approaches. A corollary of this idea is that similar binding pockets might bind the same ligand. This makes the comparison of ligand binding sites is a generally useful tool, with possible applications ranging from examining the effects of induced fit, to comparing related proteins to explore selectivity, and even searching for off-target effects or drug repurposing campaigns. We have recently applied the same shape-based approach that has proven very successful in the ligand-based virtual screening realm to this problem of binding site comparison in a new tool, SiteHopper, which can rapidly define binding sites by shape and surface chemical features. These binding site definitions, called "patches", can be collected from public or internal sources into a database, which then can be searched using as a query the specific pocket of interest, yielding a hitlist of aligned similar pockets. Due to the generality of this method, we have chosen to implement SiteHopper as a series of python scripts using the toolkits, rather than as a compiled application, to further allow modification by users to their specific needs and interests. More detail will be provided as to the specifics of the shape-based definition of a binding site, our philosophy on toolkits, and examples of possible uses for SiteHopper.
Sign in to add slides, notes or videos to this session