Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural dom ains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wid e Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain fr om each of the homologous families. This database has been derived by ident ifying the presence of structural domains in proteins on the basis of inter -secondary structural distances using the program DIAL [Sowdhamini & Blunde ll (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfami lies has been performed on the basis of the structural features and relatio nships of individual residues using the program COMPARER [Sali & Blundell ( 1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain informa tion on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed str uctures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in t he comparison of newly determined protein structures with previously identi fied protein domains or existing families.