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Nucleic Acids Research, 2003, Vol. 31, No. 1 494-498
© 2003 Oxford University Press

The PSSH database of alignments between protein sequences and tertiary structures

Andrea Schafferhans, Joachim E. W. Meyer and Seán I. O'Donoghue*

Lion Bioscience AG, Waldhoferstrasse 98, 69123 Heidelberg, Germany

*To whom correspondence should be addressed. Tel: +49 62214038363; Fax: +49 62214038201; Email: sean.odonoghue{at}lionbioscience.com

ABSTRACT

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/.


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