The HSSP data base of protein structure-sequence alignments

HSSP (homology-derived structures of groteins) is a derived data base merging information from three-dimensional structures and one-dimensional sequences of proteins. For each protein of known 3-D structure from the Brookhaven Protein Data Bank (PDB) [1] the data base has a file with all sequence homologues aligned to the PDB protein. Homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. As a result, HSSP is not only a data base of aligned sequence families, but also a data base of implied secondary and tertiary structures. Likely secondary structures can be directly carried over from the PDB protein to each homologue. Tertiary structure models can be built by fitting the sequence of the homologue, as aligned, into the 3-D template of the protein of known structure. Relative to the experimentally derived structural information in PDB, HSSP increases the number of effectively known protein structures severalfold. The database is useful for the analysis of residue conservation in structural context, for the definition of structurally meaningful sequence patterns, and for other questions of protein evolution, folding and design.