Computer Modeling of Biomolecular Systems

Period of Performance: 08/01/2004 - 07/31/2005

$375K

Phase 2 SBIR

Recipient Firm

Stewart Computational Chemistry
Colorado Springs, CO 80921
Principal Investigator

Abstract

DESCRIPTION (provided by applicant): Software for full quantum mechanics modeling of biological macromolecules that is both fast and accurate is proposed. Cancer researchers could use this software to model protein and enzyme structure as well as enzyme reactions involving bond formation and breaking. The software would be based on a semi-empirical quantum chemical compute engine with a newly developed parameterization for all biological elements including the six principal transition elements. In Phase II, the following objectives would be pursued: A. Methods specific to proteins and other biomolecules would be developed. Existing methods are (a) too general, and (b) unsuitable for biochemical work, due to the lack of transition metals. By developing semiempirical methods that are specific to systems found in biochemistry, an increase in accuracy can be obtained, thus the average error in heats of formation predicted by semiempirical methods should be decreased by about 50% relative to PM3. Average errors in geometries of biomolecules would be reduced below that of comparable semiempirical methods. Similarly, limiting the range of properties optimized for transition metals to those important in biochemical systems, an accuracy at least equivalent to ab initio 6- 31g* would be achieved. B. Writing Graphical user interfaces (GUI) and utilities to allow reactions, transition states, UV-Visible spectra, etc. to be modeled. These wilt allow users to run simulations using by issuing "requests", which the GUI will convert into commands for the compute engine. The compute engine would run at a speed sufficient to allow real-time simulations to be performed. This tool will be useful for visualizing biochemical systems, and for understanding the mechanisms involved.