NAR Molecular Biology Database Collection entry number 442

http://ekhidna.biocenter.helsinki.fi/dali/start

L. Holm

Institute of Biotechnology, University of Helsinki

Contact holm@ebi.ac.uk

The Dali database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali search engine, http://www.ebi.ac.uk/dali/.

The database currently consists of 6431 records, including all representative structures from the PDB with less than 90% sequence identity to each other (PDB90). The Fold Index lists all chains in PDB90 ordered by structural similarity. From the Fold Index, the user can browse individual entries, which comprise the list of structural neighbours and their alignments. The database can also be queried for PDB codes or protein names. Access to the database has been improved to permit fast browsing. The format of the entries has been made more human-readable and the amount of output has been limited in interactive browsing.

For non-interactive use, we provide comprehensive computer-readable database-dumps for large-scale studies. Database updates for the DaliLite program http://www.ebi.ac.uk/~holm/DaliLite/ are provided.

This database replaces the obsolete FSSP.

We are grateful to all structural biologists who deposit structures in the PDB. Many people have contributed to the Dali service over the years: Antoine de Daruvar, Chris Dodge, Kim Henrick, Dariusz Plewczynski, Chris Sander. This work was supported by the Sigfrid Juselius Foundation.

Go to the abstract in the NAR 2001 Database Issue.

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