The long term goal of this project is the development of new macromolecular modeling capabilities in PROPHET, and NIH-sponsored computer resource developed specifically for biomedical scientists. PROPHET brings modern computing tools and techniques to scientists doing research in pharmacology and related disciplines, i.e. studying the relationship between the structure of a chemical and its biological effect. An important tool for this study is the molecular mechanics method, in which the physical and chemical properties of molecular systems can be calculated from a model of the potential energy interactions between atoms. Although PROPHET has molecular mechanics capability for small molecules through an interface to the well-known MM2 program from Dr N. L. Allinger, it has limited tools for modeling large molecular systems such as DNA, RNA, and proteins. The development of an interface to the macromolecular mechanics and dynamics program, AMBER from Peter Kollman, would provide the needed capability in this area. AMBER is a well-established molecular modeling system used by hundreds of researchers. The PROPHET system is a widely used research system that offers a broad spectrum of integrated, graphics-oriented information-handling tools. PROPHET can aid research scientists in the manipulation and analysis of data through tables, statistics, and graphs, as well as the sharing of information among users. The combination of AMBER and PROPHET would provide a powerful set of software tools for macromolecular modeling and analysis that reflect current biomedical research needs. The interface developed in this work for AMBER will serve as a prototype for interfaces to other computational chemistry packages so that PROPHET can continue to evolve with the increasing sophistication of biomedicine and computer technology.
