ITR: Efficient Calculation of Molecular Surfaces

Dowling College, Oakdale NY

Investigators

Abstract

EF-0312612 Bernstein, Herbert Abstract Just a few years ago, interactive rendering of the surfaces of several hundred atoms with the best available software strained the then-available hardware. Current software technology for the rendering of molecular surfaces is slightly short of the performance needed for high-quality interactive rendering of the largest macromolecules on commonly available graphics workstations. Some of the best available packages in terms of performance are limited in their range of applications. This is the time for an aggressive push to gain the best possible software performance and the best possible coverage. This project aims to provide a significant improvement in surface-rendering algorithms by trading time for space, by changing dots and triangles to elliptical rendering elements more appropriate to this task, and by embedding an awareness of display resolution in the algorithms used. The contribution of this project is in an improved understanding of the tradeoffs among the parameters involved. The broader impacts of this effort include training of undergraduate students in the cross-disciplinary skills required for work in Bioinformatics, preparing of curriculum materials that should be of value to others teaching undergraduates and first-year graduate students such skills, increasing general awareness of the importance of the interaction of resolution considerations with analysis of algorithmic complexity in computational geometry, and increasing use of molecular surface renderings to facilitate understanding of interactions among molecules.