The search for functional correspondences in molecular structure between two dissimilar molecules

Abstract

Where structural similarities between molecular ligands are suspected in competitive binding, these similarities may be represented by a set of correspondences between analogous ligand points in the two molecules. This paper describes an algorithm which searches through all possible sets of this form, to find the one which gives the best geometric fit between matched points. Two parameters are supplied to the algorithm, giving the number of correspondences required and the tolerance permitted in the fit. A tree-search technique is used, and methods are described which prune the tree and thus limit the search. The marine neurotoxins, saxitoxin and tetrodotoxin, are used to test a computer implementation of the procedure.