Genetically Evolved Receptor Models
GERM
GERM, Genetically Evolved Receptor Models, version 3.0 is available from:
D. Eric Walters, Ph.D.
Associate Professor, Biological Chemistry
Finch University of Health Sciences/The Chicago Medical School
3333 Green Bay Road
North Chicago, IL 60064 USA
Telephone: + 1 708 578 3000, ext. 498
Fax: + 1 708 578 3240
e-mail: walterse@mis.finchcms.edu
The purpose of the GERM program is to develop three-dimensional atom-based models of previously uncharacterized receptor sites, starting from a small structure-activity series of active and inactive compounds (3 or more structures). The program is described in J. Medicinal Chem., 37, 2527-2536 (1994).
The GERM program uses a genetic algorithm to construct and improve models so that calculated drug-receptor binding energies correlate with experimentally measured bioactivities for the known series of compounds. Other structures may then be docked into the receptor site models and bioactivities may be predicted. The models can be used with other drug design software to search 3-D databases or to design de novo novel ligands.
The current version of GERM reads and writes the Quanta/CHARMm and Cerius2 file formats (Molecular Simulations Inc.); Sybyl mol2 (Tripos) files; MacroModel files; other formats may be made available on request.
Executable code for GERM is available for SGI Iris or Indigo workstations, ESV workstations, or IBM-PC/compatibles. Source code is written in ANSI C and should compile on any Unix workstation or PC. Updates will be provided for 18 months at no additional cost. Source code is provided with non-academic licenses. Documentation is provided as a hard-copy manual. GERM is supported by the author (e-mail, fax, phone).
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