ITR: Enhancing Crystal Structure Determination through Data Mining, Collaborative Environments, and Grid Computing

ITR：通过数据挖掘、协作环境和网格计算增强晶体结构测定

• 批准号: 0204918
• 负责人: Russ Miller
• 金额: --
• 依托单位: SUNY at Buffalo
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-07-01 至 2009-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0204918&HistoricalAwards=false
• 关键词: ITR; Enhancing; Crystal; Structure; Determination

ITR: Enhancing Crystal Structure Determination through Data Mining, Collaborative Environments, and Grid ComputingX-ray crystallography, with its unique ability to reveal the atomic or near-atomic structures of a wide range of biomedically important molecules, is the cornerstone of modern structural biology. This project will support critical advances in the enabling technologies of automated tuning of software, learning via data mining, geographically distributed collaborative environments, and grid computing for the enhancement and determination of crystal structure.Computer programs based on "direct methods" are used to determine the majority of small-molecule organic crystal structures. These methods begin to fail in the 100-200-atom range because the accuracy of the underlying probabilistic relationships is inversely proportional to the square root of the size of the structure. The Shake-and-Bake algorithm and SnB program have extended the size of crystal structures amenable to direct-methods phasing from 100 to 2500 atoms. SnB has also been used to increase the size of heavy-atom substructures in large proteins that can be determined from 10 to 180 Se atoms. This provides a bootstrap by which complete structures, containing hundreds of thousands of atoms, can be elucidated. Such accomplishments would have been regarded as impossible only a few years ago, and the ultimate potential of the Shake-and-Bake approach to ab initio structure determination of macromolecules is unknown.The integrated SnB collaborative environment will allow multiple simultaneous users at distinct locations to work together in a virtual environment via a variety of platforms (from 3D fully immersive to desktop PC). Users will be able to navigate through a structure, search and import structures available from public crystallographic data banks, edit structures, and interface directly with SnB while running either in solution mode or in refinement mode. The users will have the ability to work in a collaborative fashion as they would if they were all situated in close physical proximity. Finally, platforms consisting of computational grids are available in many academic and commercial institutions that use crystallographic software. A grid-enabled version of SnB will be created so that it can take advantage of computational grids and networks of workstations that have available computing cycles. The introduction of SnB has had an enormous impact on the crystallographic community. The integration of the Shake-and-Bake methodology with automated data warehousing and data mining should provide equally spectacular advances in the near future. The introduction of collaborative environments and the ability to exploit computational grids is expected to have a significant impact as well. Advances in enabling technologies coupled to a widely-distributed package, provides a unique opportunity to evaluate the viability of these enabling technologies, which have far-reaching applications to a wealth of diverse areas, including computational chemistry, advanced design, optimization, and edutainment.

ITR：通过数据挖掘、协作环境和网格计算增强晶体结构测定X射线结晶学以其独特的能力揭示一系列具有生物医学意义的重要分子的原子或近原子结构，是现代结构生物学的基石。该项目将支持在软件自动调整、通过数据挖掘学习、地理分布的协作环境和用于增强和确定晶体结构的网格计算等使能技术方面的关键进展。基于直接方法的计算机程序用于确定大多数小分子有机晶体结构。这些方法在100-200原子范围内开始失效，因为基本概率关系的精确度与结构大小的平方根成反比。Shake-and-Bake算法和SNB程序将适用于直接位相方法的晶体结构的尺寸从100个原子扩展到2500个原子。SNB还被用来增加大蛋白质中重原子亚结构的尺寸，可以确定从10个到180个Se原子。这提供了一个自助法，通过它可以阐明包含数十万个原子的完整结构。就在几年前，这样的成就还被认为是不可能的，摇晃烘焙方法在从头计算确定大分子结构方面的最终潜力是未知的。集成的SNB协作环境将允许不同地点的多个同时用户通过各种平台(从3D完全沉浸式到台式PC)在虚拟环境中共同工作。用户将能够浏览结构，搜索和导入公共晶体数据库中的结构，编辑结构，并在以解决模式或优化模式运行时直接与SNB交互。用户将能够以协作的方式工作，就像他们都位于物理上非常接近的地方一样。最后，许多使用结晶学软件的学术和商业机构都提供了由计算网格组成的平台。将创建启用网格的SNB版本，以便它可以利用具有可用计算周期的计算网格和工作站网络。SNB的引入对结晶界产生了巨大的影响。Shake-and-Bake方法与自动化数据仓库和数据挖掘的集成在不久的将来应该会带来同样惊人的进步。协作环境的引入和利用计算网格的能力预计也将产生重大影响。使能技术的进步与广泛分布的程序包相结合，为评估这些使能技术的可行性提供了独特的机会，这些使能技术具有广泛的应用，包括计算化学、高级设计、优化和教育娱乐。