Protein segment finder, or PSF, is a search engine to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints in the PDB (Protein Data Bank)
Description
Finding related conformations in the Protein Data Bank (PDB) is essential in many areas of bioinformatics. To assist this task, a search engine that uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints was designed. 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. PSF is publicly available online at http://ari.stanford.edu/psf