Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects

Relibase is a database system that has been specially designed to handle protein–ligand data. Included within Relibase is a tool that can be used to systematically analyse protein–ligand interaction patterns specified by three‐dimensional (3D) constraints, revealing favorable combinations of interacting functional groups and their preferred interaction geometries. This paper describes the Relibase 3D query tools, including novel extensions (Relibase+) for handling crystallographic packing effects. Examples illustrating the broad range of functionality for defining 3D interaction patterns and the application of such queries in drug design comprise carbonyl–carbonyl interactions, zinc binding site environments, and ligand–ligand interactions in the crystal packing. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 99–110, 2002; DOI 10.1002/bip.10075