Finding hydrophobic microdomains using an object-oriented database

A procedure for finding clusters of adjacent residues in protein hydrophobic cores--hydrophobic microdomains--has been proposed by Plochocka et al. A program is presented that finds hydrophobic microdomains, making use of protein structure data stored in an object-oriented database and the list-processing features of Prolog. Alternative definitions for hydrophobic microdomains are explored. Results are presented for haemoglobin.