Protein segment finder: an online search engine for segment motifs in the PDB.

Finding related conformations in the Protein Data Bank (PDB) is essential in many areas of bioscience. To assist this task, we designed a search engine that uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints. The database contains information such as amino acid sequence, secondary structure, disulfide bonds, hydrogen bonds and atoms in contact as calculated from all protein structures in the PDB. The search engine parses the database and returns hits that match the queried parameters. The conformation search engine, which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure. The engine is publicly available at http://ari.stanford.edu/psf and it will also be used in-house in an automatic mode aimed at discovering new protein motifs.