ROSETTA An Integrated Protein Structure Modeling Suite

ROSETTA 集成蛋白质结构建模套件

• 批准号: 7172634
• 负责人: BRIAN A KUHLMAN
• 金额: $ 64.12万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-03-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7172634
• 关键词: Address; Algorithms; Amber; Area; Arts; Code; Communities; Complex; Computer software; Custom; DNA; DNA-Protein Interaction; Development; Docking; Documentation; Elements; Future; Goals; Individual; Internet; Laboratories; Language; Libraries; Maintenance; Methodology; Methods; Modeling; Numbers; Operating System; Planning Techniques; Process; Proteins; Protocols documentation; Publishing; Range; Research; Research Personnel; Resolution; Side; Site; Software Engineering; Source Code; Specificity; Standards of Weights and Measures; Structure; System; Testing; Trees; Vertebral column; base; comparative; data structure; design; improved; model design; molecular mechanics; novel; programs; protein folding; protein structure; protein structure prediction; structural biology; syntax

DESCRIPTION (provided by applicant): The aim of this proposal is to modernize the Rosetta software package for protein structure modeling in order to facilitate its continued development in parallel in multiple research groups and to promote the widespread use of the software in the scientific community. Achieving this aim would have a very positive impact on computational structural biology quite broadly because in many critical areas, the Rosetta methodology appears to be at least as good, if not better, than other approaches. By facilitating further development and application of the software by a large group of researchers throughout the scientific community, the power and usefulness of the software should increase enormously. Rosetta currently contains modules for de novo protein structure prediction, protein design, protein-protein docking, proteinprotein and proteim DNA interface design, protein-protein and protein-DNA interaction specificity prediction, loop modeling, and high-resolution protein structure refinement. These diverse applications provide stringent tests for the underlying potential functions and optimization methods that are shared by all modules, stimulating continued improvements in both areas. When such improved core elements are incorporated into the integrated Rosetta structure-modeling platform, all the individual applications reap the benefits. Integration of the different modules in a single package has made substantial advances possible by allowing multiple modules to be combined to address complex modeling problem. For example, the combined use of the structure prediction, protein design, and model refinement modules allowed the design of a novel protein fold with atomic level accuracy. To facilitate further integration of the different modules to attack problems such as flexible backbone protein-protein docking, and to facilitate the continued development of new features and functionality, the Rosetta package will be ported to C++ and modernized to an object-oriented design. To promote widespread use of the software, a comprehensive Rosetta web server will be developed, the modernized source code will be made freely available to the scientific community with extensive documentation, and researchers throughout the community will be encouraged to join the growing Rosetta development team.

描述（由申请人提供）： 该提案的目的是将Rosetta软件包现代化用于蛋白质结构建模的软件包，以促进其在多个研究小组中并行的持续开发，并促进科学界广泛使用该软件。实现这一目标将对计算结构生物学产生非常积极的影响，因为在许多关键领域，Rosetta方法论似乎至少比其他方法一样好，甚至更好。通过促进整个科学界的大量研究人员对软件的进一步开发和应用，该软件的功能和实用性应大大增加。 Rosetta目前包含用于从头蛋白质结构预测，蛋白质设计，蛋白质 - 蛋白质对接，蛋白质蛋白质和蛋白质DNA界面设计，蛋白质 - 蛋白质和蛋白质-DNA相互作用特异性预测，Loop建模和高分辨率蛋白质结构的细化的模块。这些不同的应用程序为所有模块共享的潜在潜在功能和优化方法提供了严格的测试，从而刺激了这两个领域的持续改进。当将这种改进的核心元素纳入集成的Rosetta结构模型平台中时，所有个人应用程序都将获得收益。单个软件包中不同模块的集成通过允许组合多个模块以解决复杂的建模问题，从而实现了重大进步。例如，结构预测，蛋白质设计和模型改进模块的联合使用允许设计具有原子水平精度的新型蛋白质折叠。为了促进不同模块的进一步整合以攻击诸如柔性骨干蛋白 - 蛋白质对接等问题，并促进新功能的持续开发，Rosetta软件包将移植到C ++并将其现代化为面向对象的设计。为了促进该软件的广泛使用，将开发全面的Rosetta Web服务器，将通过广泛的文档为科学界免费提供现代化的源代码，并鼓励整个社区的研究人员加入不断增长的Rosetta开发团队。