title: Active-site-directed 3D database searching: pharmacophore extraction and validation of hits.
abstract: Two new computational tools, PRO_PHARMEX and PRO_SCOPE, for use in active-site-directed searching of 3D databases are described. PRO_PHARMEX is a flexible, graphics-based program facilitating the extraction of pharmacophores from the active site of a target macromolecule. These pharmacophores can then be used to search a variety of databases for novel lead compounds. Such searches can often generate many 'hits' of varying quality. To aid the user in setting priorities for purchase, synthesis or testing, PRO_SCOPE can be used to dock molecules rapidly back into the active site and to assign them a score using an empirical scoring function correlated to the free energy of binding. To illustrate how these tools can add value to existing 3D database software, their use in the design of novel thrombin inhibitors is described.
authors.affiliation: Proteus Molecular Design Ltd., Macclesfield, Cheshire, U.K.
authors.forename: D E
authors.initials: DE
authors.lastname: Clark
authors.forename: D R
authors.initials: DR
authors.lastname: Westhead
authors.forename: R A
authors.initials: RA
authors.lastname: Sykes
authors.forename: C W
authors.initials: CW
authors.lastname: Murray
mesh_terms: D001665:Binding Sites; D003196:Computer Graphics; D003198:Computer Simulation; D017076:Computer-Aided Design; D016208:Databases, Factual; D015195:Drug Design; D046911:Macromolecular Substances; D008958:Models, Molecular; D015394:Molecular Structure; D012984:Software
chemical_list: D046911:Macromolecular Substances