Database structure and searching in MACCS-3D

Abstract

The MACCS-3D program was developed to provide a three-dimensional (3D) structural database system for structure, substructure, geometric, and data searching purposes. Applications of the program include discovery of new drugs and agrochemicals to fit known or postulated pharmacophores, and identification of polymers and commercial chemicals whose physical and chemical properties depend on 3D structural features. This paper presents details of the data structures and algorithms used for 3D structural representation, storage, and searching in MACCS-3D. These include algorithms for exact match, substructure, geometric, submodel, and combined 3D structure-data searching. We also describe mechanisms used for 3D data storage and geometric search keys. Integration of MACCS-3D with new chemical representation and search capabilities of the MACCS-II system are briefly described. Finally, new developments in MACCS-3D are described, in light of current and future trends in 3D searching.