A novel search method for protein sequence--structure relations using property profiles.

In protein engineering and design it is very important that residues can be inspected in their specific environment. A standard relational database system cannot serve this purpose adequately because it cannot handle relations between individual residues. With SCAN3D we introduce a new database system for integrated sequence and structure analysis of proteins. It uses the relational paradigm wherever possible. Its main power, however, stems from the ability to retrieve stretches of consecutive residues with certain properties by comparing a property profile with all stretches of residues in the database, exploiting the ordered character of proteins. In doing so, it bypasses the large number of join operations that would be required by relational database systems. An additional advantage of using property profile matching is that searches can be carried out allowing a pre-set number of mismatches. Also, as the database is read-only, SCAN3D does not need interactive data update mechanisms. Queries typical of a molecular engineering environment are demonstrated with specific examples: analysis of peptides that induce local structure, analysis of site-dependent rotamers and residue--residue contact analysis.