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Nucleic Acids Research, 2002, Vol. 30, No. 1 200-202
© 2002 Oxford University Press

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro

Vadim P. Valuev*, Dmitry A. Afonnikov, Mikhail P. Ponomarenko, Luciano Milanesi1 and Nikolay A. Kolchanov

Institute of Cytology and Genetics, Lavrentieva ave. 10, Novosibirsk 630090, Russia and 1Istituto Tecnologie Biomediche Avanzate, Via Fratelli Cervi 93, 20090 Segrate, Italy

ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution processes (mainly by means of phage display). At present, the ASPD database contains data on 195 selection experiments, which were described in 112 original papers. For each experiment, the following information is given: (i) description of the target for binding, (ii) description of the protein or peptide which serves as the template for library construction and description of the native protein which binds the target, (iii) links to the major proteomic databases (SWISS-PROT, PDB, PROSITE and ENZYME), (iv) keywords referring to the biological significance of the experiment, (v) aligned sequences of proteins or peptides retrieved through in vitro evolution and relevant native or constructed sequences, (vi) the number of rounds of selection/amplification and (vii) the number of occurrences of clones with each sequence. The literature data include a full reference, a link to the MEDLINE database and the name of the corresponding author with his email address. ASPD has a user-friendly interface which allows for simple queries using the names of proteins and ligands, as well as keywords describing the biological role of the interaction studied, and also for queries based on authors’ names. It is also possible to access the database by means of the SRS system, allowing complex queries. There is a BLAST search tool against the ASPD for looking directly for homologous sequences. Research tools of the ASPD allow the analysis of pairwise correlations in the sequences of proteins and peptides selected against one target. The URL for the ASPD database is http://www.sgi.sscc.ru/mgs/gnw/aspd/.

* To whom correspondence should be addressed. Tel: +7 383 233 2971; Fax: +7 383 233 1278; Email: valuev{at}bionet.nsc.ru


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