Rapid Comparison of Protein Binding Sites
Comparing protein binding sites is an important method in drug discovery that plays a part in a wide variety of structure-centric pursuits. One challenge for binding site comparison methods is the broad goals of such approaches: from identifying subtle differences between largely similar sites in induced fit analysis or understanding selectivity, to identifying general similarity for drug repurposing or target fishing searches.
SiteHopper represents an application of the Shape and Color approach that has been so successful in ROCS to the domain of protein comparison. Treating binding sites as constructs with a defined shape and set of chemical features allows for rapid searching of database of known structures (internal or public) as well as more advanced applications such as clustering.
Due to the general nature of binding site comparison, SiteHopper is implemented as a toolkit application in Python. This provides users the ability to examine and modify the source code to optimize the approach to a specific use. The ability to create a focused application through combining the OEChem, Shape, and Spicoli toolkits demonstrates the power of the OpenEye Toolkit Platform for rapid development of new computational approaches.