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X射线晶体学以其独特的能力揭示了广泛的生物医学重要分子的原子或近原子结构，是现代结构生物学的基石。该项目将支持自动调整软件、通过数据挖掘学习、地理分布协作环境和网格计算等使能技术的关键进展，以增强和确定晶体结构。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。这些方法开始在100-200个原子的范围内失败，因为潜在的概率关系的精度与结构尺寸的平方根成反比。Shake-and-Bake算法和SnB程序已经将适合于直接定相方法的晶体结构的大小从100个原子扩展到2500个原子。SnB也被用于增加大蛋白质中重原子亚结构的大小，可以从10到180个Se原子确定。这提供了一个引导程序，通过它可以阐明包含数十万个原子的完整结构。这些成就在几年前还被认为是不可能的，而Shake-and-Bake方法在大分子从头计算结构测定中的最终潜力尚不清楚。集成的SnB协作环境将允许不同位置的多个用户通过各种平台（从3D完全沉浸式到桌面PC）在虚拟环境中一起工作。用户将能够在结构中导航、搜索和导入公共晶体学数据库中可用的结构、编辑结构，并在解决方案模式或细化模式下运行时直接与SnB接口。用户将有能力以协作的方式工作，就像他们都位于物理接近的位置一样。最后，由计算网格组成的平台在许多使用晶体学软件的学术和商业机构中可用。将创建SnB的网格启用版本，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的引入对晶体学界产生了巨大的影响。在不久的将来，将“摇晃和烘烤”方法与自动化数据仓库和数据挖掘相结合，将带来同样引人注目的进步。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软件包相结合，为评估这些使能技术的可行性提供了独特的机会，这些技术在计算化学、先进设计、优化和寓教于乐等众多领域都有着深远的应用。

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.