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.
Bergner
A
A
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom. bergner@ccdc.cam.ac.uk
Günther
J
J
Hendlich
M
M
Klebe
G
G
Verdonk
M
M
D001665:Binding Sites; D003208:Concanavalin A / Q000737:chemistry; D018360:Crystallography, X-Ray; D019992:Databases as Topic; D019427:HIV Integrase / Q000737:chemistry; D007091:Image Processing, Computer-Assisted; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism; D012984:Software; D013223:Statistics as Topic; D015032:Zinc
D008024:Ligands; D011506:Proteins; D003208:Concanavalin A; D019427:HIV Integrase; D015032:Zinc