Identification of protein binding surfaces using surface triplet propensities

摘要

Motivation: The ability to reliably predict protein–protein and protein–ligand interactions is important for identifying druggable binding sites and for understanding how proteins communicate. Most currently available algorithms identify cavities on the protein surface as potential ligand recognition sites. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule. A total of 455 different types of triplets can be identified. A training set of 309 protein–ligand protein X-ray structures has been used to generate interface propensities for the triplets, which can be used to predict their involvement in ligand–binding interactions.