ITR: Efficient Calculation of Molecular Surfaces

就在几年前，用最好的可用软件对数百个原子的表面进行交互渲染，使当时可用的硬件变得紧张。目前用于绘制分子表面的软件技术略低于在常见的图形工作站上高质量地交互绘制最大的大分子所需的性能。就性能而言，一些可用的最佳包在其应用程序范围内是有限的。现在是积极推进以获得尽可能最佳的软件性能和尽可能好的覆盖面的时候了。该项目旨在通过以时间换取空间，通过将点和三角形更改为更适合此任务的椭圆渲染元素，以及通过在所使用的算法中嵌入显示分辨率的意识，来显著改进表面渲染算法。这个项目的贡献在于更好地理解了所涉及的参数之间的权衡。这一努力的更广泛影响包括对本科生进行生物信息学工作所需的跨学科技能的培训，准备对其他人应该有价值的课程材料，教授本科生和一年级研究生此类技能，提高对解析考虑与计算几何中算法复杂性分析相互作用的重要性的普遍认识，以及更多地使用分子表面渲染来促进理解分子之间的相互作用。

EF-0312612Bernstein, HerbertAbstractJust 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.