Research Project
3502809
(Adapted from Applicant's Abstract) The applicant proposes to develop software for a personal computer in which the user can interactively display the three-dimensional structure of docked biomolecules, including proteins and nucleic acids, and simultaneously display the energetic properties of the docking interaction. In its simplest application the software would allow the user, starting from the downloaded coordinates, to compute and display physical properties of individual biomolecules, including surrounding electrostatic fields and other quantities. In its most advanced application an exhaustive search of plausible low energy protein-ligand, protein-protein or protein-DNA docking complexes would be generated using a Brownian dynamics algorithm. This method would exploit an automated force-guided search would avoid trapping in local energy minima, and would further allow the user to manipulate the conformers with full energy monitorization. Phase I will demonstrate whether such sophisticated code: (a) can be integrated to run on a personal computer; (b) can withstand the simplifying approximations necessary to adapt it to this environment; and (c) can accurately reproduce results obtained by mainframes. This Phase-I version (for use on proteins) would be generalized in Phase II to nucleic acids with the inclusion of additional user-friendly front-end interfacing.
