StructSorter: a method for continuously updating a comprehensive protein structure alignment database

Advances in protein crystallography and homology modeling techniques are producing vast amounts of high resolution protein structure data at ever increasing rates. As such, the ability to quickly and easily extract structural similarities is a key tool in discovering important functional relationships. We report on an approach for creating and maintaining a database of pairwise structure alignments for a comprehensive database comprising the PDB and homology models for the human and select pathogen genomes. Our approach consists of a novel, multistage method for determining pairwise structural similarity coupled with an efficient clustering protocol that approximates a full NxN assessment in a fraction of the time. Since biologists are commonly interested in recently released structures, and the homology models built from them, an automatically updating database of structural alignments has great value. Our approach yields a querying system that allows scientists to retrieve databank-wide protein structure similarities as easily as retrieving protein sequence similarities via BLAST or PSI-BLAST. Basic, noncommercial access to the database can be requested at https://tip.eidogen-sertanty.com/.