TGSA: A molecular superposition program based on topo-geometrical considerations

Abstract

In this article, a new molecular alignment procedure to provide general-purpose, fast, automatic, and user-intuitive three-dimensional molecular alignments is presented. This procedure, called Topo-Geometrical Superposition Approach (TGSA), is only based on comparisons of atom types and interatomic distances; hence, the procedure can handle large molecular sets within affordable computational costs. The method is able to accurately align 3D structures using the common molecular substructures, as inferred by the bonding pattern (atom correspondences), where present. The algorithm has been implemented into a program named TGSA99, and it has been tested over eight different molecular sets: flavilium salts, amino acids, indole derivatives, AZT, steroids, anilide derivatives, poly-aromatic-hydrocarbons, and inhibitors of thrombine. The TGSA algorithm performance is evaluated by means of computational time, number of superposed atoms, and index of fit between the compared structures. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 255–263, 2001