Rosetta: An Integrated Macromolecular Modeling Suite

Rosetta：集成的大分子建模套件

• 批准号: 8729395
• 负责人: BRIAN A KUHLMAN
• 金额: $ 53.01万
• 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 2017-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8729395
• 关键词: Acquired Immunodeficiency Syndrome; Affect; Algorithms; Architecture; Back; Benchmarking; Biological; Biosensor; Code; Communities; Complex; Computer software; Computers; Custom; DNA; Development; Docking; Educational process of instructing; Educational workshop; Ensure; Environment; Extensible Markup Language; Funding; Goals; Growth; Human; Internet; Knowledge; Laboratories; Libraries; Licensing; Life; Maintenance; Malignant Neoplasms; Modeling; Molecular Models; Molecular Structure; NIH Program Announcements; Occupations; Output; Protein Binding; Protein Engineering; Proteins; Protocols documentation; Pythons; RNA; Research; Research Personnel; Resources; Running; Sampling; Schedule; Scientist; Source Code; Speed; Structure; System; Testing; Training; Universities; Work; Workplace; base; cellular imaging; computer cluster; computer program; design; fighting; flexibility; human disease; inhibitor/antagonist; macromolecule; microbial alkaline proteinase inhibitor; molecular modeling; monomer; parallel computer; pathogen; programs; protein structure prediction; public health relevance; response; scaffold; scripting interface; simulation; three dimensional structure; tool; vaccine development

DESCRIPTION (provided by applicant): Rosetta is molecular modeling software that has been developed for the prediction and design of macromolecular structure. Rosetta has performed well in community wide assessments of protein structure prediction and docking, and it has been used to engineer proteins for a variety of applications including: scaffold design for vaccine development, biosensor design for live cell imaging, and protein interface design to create inhibitors of human pathogens. Rosetta is developed and maintained by research groups at over 20 universities, and over the 9 years since its first release, 9750 academic laboratories have obtained free licenses to use the software. This proposal is a competing renewal and is in response to a program announcement (PAR-11-028) for the continued development and maintenance of software. Activities from the previous funding periods have been instrumental in the productive growth of Rosetta, these include the creation of a C++ object-oriented version of Rosetta (from Fortran) that allows scientists to more easily combine alternate sampling protocols and energy functions, the development of an automated testing system for checking the integrity of the code base, deployment of web servers for more standard Rosetta simulations, and user support through an online forum system. With this proposal our goal is to further increase the usefulness of Rosetta to expert and non-expert users as well as promote the rapid development of new algorithms by maintaining a robust code base and a rigorous set of technical and scientific benchmarks. Our specific aims include the further development and extension of scripting tools for generating custom protocols, increasing the speed of Rosetta simulations through parallel computing, deployment of new automated tests to validate code accuracy and enforce coding standards, and user support through a unified web server for Rosetta applications.

描述（由申请人提供）：Rosetta 是为大分子结构的预测和设计而开发的分子建模软件。 Rosetta 在蛋白质结构预测和对接的全社区评估中表现良好，它已被用于工程蛋白质以用于各种应用，包括： 疫苗支架设计 开发、活细胞成像生物传感器设计以及创建人类病原体抑制剂的蛋白质界面设计。 Rosetta 由 20 多所大学的研究小组开发和维护，自首次发布以来的 9 年来，已有 9750 个学术实验室获得了使用该软件的免费许可证。该提案是一项竞争性更新，是对软件持续开发和维护的计划公告 (PAR-11-028) 的回应。之前资助期间的活动对 Rosetta 的生产力增长发挥了重要作用，其中包括创建 Rosetta 的 C++ 面向对象版本（来自 Fortran），使科学家能够更轻松地将替代采样协议和能量函数结合起来，开发用于检查代码库完整性的自动测试系统、用于更标准 Rosetta 模拟的 Web 服务器部署以及通过在线论坛系统提供的用户支持。通过这项提案，我们的目标是进一步提高 Rosetta 对专家和非专家用户的实用性，并通过维护强大的代码库和一套严格的技术和科学基准来促进新算法的快速开发。我们的具体目标包括进一步开发和扩展用于生成自定义协议的脚本工具、通过并行计算提高 Rosetta 模拟的速度、部署新的自动化测试来验证代码准确性和执行编码标准，以及通过统一的 Web 服务器为用户提供支持罗塞塔应用程序。