Building 3D structural databases: Experiences with MDDR-3D and FCD-3D

Abstract

The process of building large three-dimensional (3D) structural databases of commercial quality presents several unique challenges. The concerns which must be faced include database size, method of 3D structure generation, batch implementation of modeling and registration, correspondence with two-dimensional structures, and quality assurance of the resulting 3D structures. We describe procedures which were developed to build two databases with CONCORD: MACCS-II Drug Data Report-3D (MDDR-3D) and Fine Chemicals Directory-3D (FCD-3D). These procedures were developed to overcome limitations in the modeling process and to increase the efficiency and reliability of registration. This paper describes these programs and techniques, and reports on their performance in building large 3D structural databases.