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Nucleic Acids Research 2005 33(Database Issue):D219-D222; doi:10.1093/nar/gki043
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Nucleic Acids Research, 2005, Vol. 33, Database issue D219-D222
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

S4: structure-based sequence alignments of SCOP superfamilies

James Casbon and Mansoor A. S. Saqi*

Institute for Cell and Molecular Science, Bart's and The London, Queen Mary's School of Medicine and Dentistry, University of London, 32 Newark Street, London E1 2AA, UK

* To whom correspondence should be addressed. Tel: +44 20 7377 0444; Fax: +44 20 7247 3428; Email: m.saqi{at}qmul.ac.uk

Received August 12, 2004; Revised and Accepted September 28, 2004

S4 is an automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database. All structural domains that do not share more than 40% sequence identity as defined by the ASTRAL compendium of protein structures are included. The alignments are constructed using pairwise structural alignments to generate residue equivalences that are then integrated into multiple alignments using sequence alignment tools. We describe the database and give examples showing how the automatically generated S4 alignments compare favourably to hand-crafted alignments. Available at: http://compbio.mds.qmw.ac.uk/S4.html.

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