Software tools for analysis and visulaization of protein structure

描述(由申请人提供)：该项目包括与蛋白质结构相关的软件工具的持续开发、评估、维护、分发和支持。RasterSD包中广泛使用的结构可视化工具将更新以在当前操作系统上使用，并进行扩展以纳入由新一代分析工具实现的新可视化模式。该小组向广大研究界提供的现有网上服务(WebTools、Parvati、TLSMD)将得到更新，服务器容量将扩大。该项目的一个主要目标是进一步扩展和分发最近开发的TLSMD软件包，用于直接从先前精炼的单晶结构推断蛋白质的柔韧性和其他动态性质。核心软件组件将被改装成标准蛋白质结晶学软件包，以便TLSMD分析可以在当地结晶学研究小组安装和使用。中央TLSMD服务器将进行扩展，以满足其他领域研究人员的需求，这些研究人员预计不会在当地安装结晶学软件。核心的TLSMD算法将被扩展和调整，以用于最初开发的晶体细化应用程序之外的应用程序。特别是，它将被扩展到生成用于蛋白质-配体和蛋白质-蛋白质对接计算的蛋白质柔性模型。这些分析技术将被应用于蛋白质数据库中的所有结构，以建立隐含结构域运动、铰链点和动力学行为的综合数据库。作为这项工作的一部分开发的算法和计算工具将免费分发，我们将提供基于网络的最先进的结构分析，由外部研究人员提交。

DESCRIPTION (provided by applicant): This project encompasses the continued development, evaluation, maintenance, distribution, and support of software tools relating to protein structure. The widely-used structural visualization tools in the RasterSD package will be brought up to date for use on current operating systems, and extended to incorporate new visualization modes made possible by a new generation of analysis tools. Existing web-based services provided by this group to the research community at large (WebTools, Parvati, TLSMD) will be updated and server capacity expanded. A major goal of the project is to further extend and distribute the recently developed TLSMD software package for the inference of protein flexibility and other dynamic properties directly from previously refined single crystal structures. The core software components will be adapted for incorporation into standard protein crystallographic packages so that TLSMD analysis may be installed and used locally crystallographic research groups. The central TLSMD server will be expanded to handle the demands of researchers in other fields, who are not expected to have crystallographic software installed locally. The core TLSMD algorithms will be extended and adapted for use outside the applications in crystallographic refinement for which it was originally developed. In particular, it will be extended to generate models of protein flexibility for use in protein-ligand and protein-protein docking calculations.These analytical techniques will be applied to all structures in the Protein Data Bank in order to build a comprehensive database of implied domain motions, hinge points, and dynamic behavior. The algorithms and computation tools developed as part of this work will be distributed freely, and we will provide web-based state of the art analysis of structures submitted by external researchers.