|
|
|
|
Brief manual on the database ASPD (Artificial Selected Peptides/Proteins Database)Enter the database ASPD here. It works under the SRS system. IntroductionASPD 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 fieldsASPD_ALIGN Identifier , Lit_reference, Target, Template, Keywords, Link, Comment, Consensus, Number, AlignmentFields descriptionIdentifier Unique identifier of an entry. It has the format PH1XXNNN, where X is a letter of latin alphabet, N is a number (0-9) Lit_reference Link to the literary reference in the ASPD_REF database (the identifier of the corresponding entry in ASPD_REF having the form PH4XXNNN) Target Target - the substrate for binding to which the peptides or proteins were selected (free text) Template Template - the native protein or peptide performing the function for which peptides from random pool were selected (free text) Keywords A list of keywords (separated with commas) describing the biological relevance of the entry. Link 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. Comment The referent's comments concerning conditions of the experiment (free text) Consensus The general form of peptides retrieved by in vitro evolution (in PROSITE signature), usally provided by the authors of the original paper. Number Number of different amino acid sequences in the entry Alignment Author's alignment of amino acid sequences (those retrieved from random pools are denoted with numbers, others (native or constructed) with letters.
ASPD_REF Identifier , Authors, Title, Journal, Volume, Year, Pages, Medline, Corresponding_Author |
