The PSSH database of alignments between protein sequences and tertiary structures

We introduce the PSSH ( Protein Sequence- to-Structure Homologies) database derived from HSSP2, an improved version of the HSSP ( Homology- derived Secondary Structure of Proteins) database [ Dodge et al. ( 1998) Nucleic Acids Res., 26, 313 - 315]. Whereas each HSSP entry lists all protein sequences related to a given 3D structure, PSSH is the inverse, with each entry listing all structures related to a given sequence. In addition, we introduce two other derived databases: HSSPchain, in which each entry lists all sequences related to a given PDB chain, and HSSPalign, in which each entry gives details of one sequence aligned onto one PDB chain. This re- organization makes it easier to navigate from sequence to structure, and to map sequence features onto 3D structures. Currently ( September 2002), PSSH provides structural information for over 400 000 protein sequences, covering 48% of SWALL and 61% of SWISS- PROT sequences; HSSPchain provides sequence information for over 25 000 PDB chains, and HSSPalign gives over 14 million sequence- to-structure alignments. The databases can be accessed via SRS 3D, an extension to the SRS system, at http: / / srs3d. ebi. ac. uk/.