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Nucleic Acids Research, 2004, Vol. 32, Database issue D203-D207
© 2004 Oxford University Press

HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database

Lucy A. Stebbings* and Kenji Mizuguchi

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK

*To whom correspondence should be addressed. Tel: +44 1223 760469; Fax: +44 1223 766002; Email: homstrad{at}cryst.bioc.cam.ac.uk

HOMSTRAD (http://www-cryst.bioc.cam.ac.uk/ homstrad/) is a collection of protein families, clustered on the basis of sequence and structural similarity. The database is unique in that the protein family sequence alignments have been specially annotated using the program, JOY, to highlight a wide range of structural features. Such data are useful for identifying key structurally conserved residues within the families. Superpositions of the structures within each family are also available and a sensitive structure-aided search engine, FUGUE, can be used to search the database for matches to a query protein sequence. Historically, HOMSTRAD families were generated using several key pieces of software, including COMPARER and MNYFIT, and held in a number of flat files and indexes. A new relational database version of HOMSTRAD, HOMSTRAD BETA (http://www-cryst.bioc.cam. ac.uk/homstradbeta/) is being developed using MySQL. This relational data structure provides more flexibility for future developments, reduces update times and makes data more easily accessible. Consequently it has been possible to add a number of new web features including a custom alignment facility. Altogether, this makes HOMSTRAD and its new BETA version, an excellent resource both for comparative modelling and for identifying distant sequence/structure similarities between proteins.


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