Rapid Computational Analysis of Biomolecular Properties

生物分子特性的快速计算分析

• 批准号: 9207256
• 负责人: Barry Honig
• 金额: $ 72.1万
• 依托单位: Columbia University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1992
• 资助国家: 美国
• 起止时间: 1992-12-01 至 1996-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9207256&HistoricalAwards=false
• 关键词: Rapid; Computational; Analysis; Biomolecular; Properties

This award will support the development of new algorithms for the rapid analysis of macromolecular conformation and for their integration into the Graphical Representation and Analysis of Surface Properties (GRASP) computer program. GRASP was designed as a research tool to facilitate the analysis of the structural and energetic properties of proteins and nucleic acids. The program is distinct from existing ones in that it allows rapid evaluation of conformational and binding energies based entirely on physical properties that can be mapped onto the molecular surface. This in turn is represented using a fast surface rendering algorithm, for display and manipulation by graphics workstations. The underlying scientific component of this project is based on the ability to calculate the conformational and biding free energies of macromolecules by using a continuum treatment of solvent. GRASP will exploit a new version of the DelPhi program for electrostatics and a new treatment of the hydrophobic effect which evaluates the relevant interactions based on surface area and curvature. When combined with a traditional "gas phase" force field, these methods should allow a complete evaluation of free energies including solvent effects. We plan to develop algorithms which make it possible to carry out accurate calculations in relatively short periods of time. By fully integrating them into GRASP we intend to make these methods available to the scientific community. The graphical component of GRASP emphasizes the mapping of all physical properties onto the molecular surface. This ability gives researchers the potential to obtain novel insights into protein and nucleic acid structure and design. The fact that it will run on graphics workstations implies that its capabilities will be readily available to a large number of researchers in the biological and chemical communities.

该奖项将支持开发新算法，以快速分析大分子构象，并将其整合到表面特性（GRASP）计算机程序的图形表示和分析中。 GRASP被设计为一种研究工具，可促进蛋白质和核酸的结构和能量特性的分析。 该程序与现有程序不同，因为它允许完全基于可以映射到分子表面的物理特性的构象和结合​​能的快速评估。 反过来，这是使用快速的表面渲染算法表示的，用于通过图形工作站的显示和操纵。 该项目的基本科学组成部分是基于使用溶剂的连续处理来计算大分子的构象和自由能的能力。 GRASP将利用Delphi程序的新版本用于静电和疏水效应的新处理方法，该方法根据表面积和曲率评估相关相互作用。 当与传统的“气相”力场结合使用时，这些方法应允许对包括溶剂效应在内的自由能进行完整评估。 我们计划开发算法，使得在相对较短的时间内进行准确的计算是可能的。 通过将它们完全集成到掌握中，我们打算将这些方法提供给科学界。 GRASP的图形成分强调了所有物理特性在分子表面上的映射。 这种能力使研究人员有潜力获得对蛋白质和核酸结构和设计的新见解。 它将在图形工作站上运行的事实意味着，生物学和化学群落中的许多研究人员将很容易获得其功能。