Brief manual on the database ASPD (Artificial Selected Peptides/Proteins Database)
ASPD is a curated database on selected from randomized pools proteins and peptides designed for accumulation of experimental data on protein functionality obtained by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) These processes imply several rounds of enrichment and amplification to obtain only those molecules with desired property. They allows for testing of large pool of molecules (up to 1013) at the same time. The most widely used technique for in vitro selection of proteins and peptides is phage display. Sequences are expressed as fusions either to gene VIII (present in several thousand copies) or to gene III (having few copies) of the phage capsid. Molecules are selected by affinity panning on immobilized substrates or receptors, and bound phage are mixed with bacteria to produce progeny for subsequent rounds. This technique with various improvements was applied to pursue a number of goals, including selection for thermodynamically more stable proteins, engineering of proteins with new or improved enzymatic activities, mapping epitopes and binding sites, finding substrates for enzymes, selecting antibodies, finding small peptide mimetics for large protein molecules etc.
The database also contains modules for pairwise correlation analysis and BLAST search.
The detailed description of the fields is given below.
Complete list of the fields
Identifier, Lit_reference, Target, Template, Keywords, Link, Comment, Consensus, Number, Alignment
Unique identifier of an entry. It has the format PH1XXNNN, where X is a letter of latin alphabet, N is a number (0-9)
Link to the literary reference in the ASPD_REF database (the identifier of the corresponding entry in ASPD_REF having the form PH4XXNNN)
Target - the substrate for binding to which the peptides or proteins were selected (free text)
Template - the native protein or peptide performing the function for which peptides from random pool were selected (free text)
A list of keywords (separated with commas) describing the biological relevance of the entry.
Links to external databases. Has the form Link DbName EntryId, where the DbName is one of the following: SwissProt, Prosite, PDB, Enzyme, and EntryId is the identifier of the corresponding entry in these databases.
The referent's comments concerning conditions of the experiment (free text)
The general form of peptides retrieved by in vitro evolution (in PROSITE signature), usally provided by the authors of the original paper.
Number of different amino acid sequences in the entry
Author's alignment of amino acid sequences (those retrieved from random pools are denoted with numbers, others (native or constructed) with letters.
Identifier, Authors, Title, Journal, Volume, Year, Pages, Medline, Corresponding_Author