NAR Molecular Biology Database Collection entry number 308
Valuev, V.P., Afonnikov D.A., Ponomarenko M.P., Kolchanov N.A.
Institute of Cytology and Genetics, Novosibirsk, Russia
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 process (mainly by means of phage display technique). ASPD database is being compiled by curating the scientific literature. At present, it contains data on 200 selection experiments, which were described in 150 original papers. For each experiment, the following information is given: description of the target for binding; description of the protein or peptide which serves as the template for library construction and description of the native protein which binds the target; links to the major proteomic databases â€“ SwissProt, PDB, Prosite and Enzyme; keywords referring to the biological significance of the experiment; aligned sequences of proteins or peptides retrieved through in vitro evolution and relevant native or constructed sequences; the number of rounds of selection/amplification cycles and the number of occurences of clones with each sequence. The literature data include full reference, link to Medline database and the name of corresponding author with his e-mail. 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 author names. The other possibility to access the database is that by means of the SRS system which allows complex queries. There is also a BLAST search tool against the ASPD for looking directly for homologous sequences. Direct data submission to the ASPD is welcome via the submission form available at the ASPD Web-page. Research tools of the ASPD comprise the analysis of pairwise correlations in the alignment of sequences of proteins and peptides selected against one target. We have calculated such correlations in terms of hydrophobicity , polarity, volume and isoelectric point. The amino acid similarity matrix based on the data stored in the ASPD was also derived and compared with other similar matrices.
The work was supported by grant No. 00-04-49229 (and its subgrant 01-04-06240) from Russian Foundation for Basic Research and grant YSF 00-177 from INTAS.
Category: Nucleotide Sequence Databases
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