CONFORMATIONAL FREEDOM IN 3-D DATABASES .1. TECHNIQUES

With the advent of databases capable of storing full 3-D information on chemical structures, it is now feasible to search such databases for particular 3-D spatial arrangements of atoms or groups (pharmacophores). This is of particular importance in drug design where the pharmacophore responsible for activity is either already known or can be deduced by standard modeling techniques. Since many of the molecules to be searched are flexible, there is a need to allow for conformational freedom within the database system and to couple it closely to modeling software for further analysis. In this paper, part 1 of a series, we will discuss some techniques that can be used to accomplish these goals as exemplified by the ChemDBS-3D module of the Chem-X modeling suite. Subsequent papers will give details of case studies performed with this system. © 1990, American Chemical Society. All rights reserved.