A PROCEDURE FOR DETECTING STRUCTURAL DOMAINS IN PROTEINS

A procedure is described for detecting domains in proteins of known st ructure. The method is based on the intuitively simple idea that each domain should contain an identifiable hydrophobic core. By applying th e algorithm described in the companion paper (Swindells MB, 1995, Prot ein Sci 4:93-102) to identify distinct cores in multidomain proteins, one can use this information to determine both the number and the loca tion of the constituent domains. Tests have shown the procedure to be effective on a number of examples, even when the domains are discontin uous along the sequence. However, deficiencies also occur when hydroph obic cores from different domains continue through the interface regio n and join one another.