Automatic Identification of Key Sub-Structures for Protein Annotation

We present a novel algorithm designed to find common sub-structure features between multiple proteins with similar function but different overall fold. The algorithm is intended to run with multiple input proteins and will find multiple matching sub-structures if there are several present. Such sub-structures would be useful in the annotation of new protein structures with unknown function, especially those without known homologues. The algorithm is independent of sequence and may take whole structures as input with no limitation on the overall size of matching patterns. We demonstrate the algorithm running on two whole adenine-binding protein structures, successfully identifying their active sites as the common substructures between them.