We have written a computer program to aid in the identification of interaction sites between proteins. The program compares the hydropathic profiles of the two interacting proteins and reports sites, demonstrating an exact pattern of inverted hydropathy. If these regions are surface accessible in the folded proteins, they are considered putative binding or docking sites and can be tested as such. In this report, we apply this program to the localization of residues involved in the anti-idiotope of a monoclonal antibody (mAb), F30C7. The anti-idiotope of F30C7 partially resembles the structure of the peptide antigen, human myelin basic protein (MBP) acetyl 1-9, used to elicit the idiotope bearing mAbs (Ab1). The sequences of F30C7 variable regions are compared to the variable regions of Ab1, as well as to the peptide antigen used to elicit F30C7. Sites of hydropathic cornplementarity In F30C7 with Ab1 that also have sequential homology with MBP 1-9 were located, and a synthetic peptide designed from these sequences was found to structurally resemble MBP 1-9 in that it: (i) inhibited Ab1 binding to MBP 1-9 and (ii) partially inhibited the binding of F30C7 to Ab1. Thus the portion of the anti-idiotope of F30C7 resembling MBP 1-9 was determined with the aid of this program. Other hits between F30C7 and Ab1 also occurred, and future studies will determine whether or not these sites might further contribute to the anti-idiotope. © 1994 Academic Press. All rights reserved.