SI2-SSE: Software Tools for Biomolecular Free Energy Calculations

SI2-SSE：生物分子自由能计算软件工具

• 批准号: 1148144
• 负责人: Celeste Sagui
• 金额: $ 49.78万
• 依托单位: North Carolina State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-07-01 至 2016-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1148144&HistoricalAwards=false
• 关键词: SI2; SSE; Software; Tools; Biomolecular

TECHNICAL SUMMARYThe Office of Cyberinfrastructure, Division of Materials Research, Chemistry Division, and Division of Civil, Mechanical, and Manufacturing Innovation contribute funds to this award made on a proposal to the Software Infrastructure for Sustained Innovation solicitation. This award supports the development of a new set of software tools for calculating biomolecular free energies, transition paths, and reaction rates that will be based on and will augment the PIs' ABMD/REMD/SMD suite of codes. New capabilities are to be added to the existing codes, which should greatly enhance the applicability of the software to challenging biomolecular problems. In particular, the PIs aim to implement and develop: (i) the capability for dealing with dynamically coupled multiple walkers or replicas for enhanced sampling; (ii) the introduction of Transition Path Theory and Sampling methodology for calculating reaction rates and related physical quantities; and (iii) the introduction of the "string method" for multi-dimensional free energy calculations and the calculation of the important minimum free energy path. These software tools will be released under the open source GPL, and released as part of the AMBER software package. The codes will also be released as stand-alone modules via the web for other users to integrate into their own programs.To test and showcase the workings of the software package, the PIs will apply these methods to biomolecular systems where changes in handedness play an important role, including: proline-rich systems, mainly collagen and a new class of cell-penetrating peptides, and DNA and RNA in B and Z double helices. This award will also enhance education through: the mentoring and recruitment of minority students, the development of a Biophysics option, the integration of research topics into current educational forums, working with local schools, and the development of a new Institute for Computational Science and Engineering.NON-TECHNICAL SUMMARYThe Office of Cyberinfrastructure, Division of Materials Research, Chemistry Division, and Division of Civil, Mechanical, and Manufacturing Innovation contribute funds to this award made on a proposal to the Software Infrastructure for Sustained Innovation solicitation. This award supports the development of a new set of software tools that will enable the calculation of rates of chemical reactions involving biomolecules. The codes will also be able to calculate the energy that can be converted into useful work in a biochemical system. The codes will be distributed through a widely used software package called AMBER which contributes to the software cyberinfrastructure of computational chemistry, biochemistry, chemical engineering, materials, and biological physics communities. It will enable a wide range of computational research involving biological molecules. Among the possible applications are the study of the structure and transformations of biomolecules which provides information on their possible functions, the simulation of antibiotics, and simulating nanoscale technology applications. This award will also enhance education through: the mentoring and recruitment of minority students, the development of a Biophysics option, the integration of research topics into current educational forums, working with local schools, and the development of a new Institute for Computational Science and Engineering.

技术摘要网络基础设施办公室，材料研究部，化学部和土木，机械和制造创新部为该奖项提供资金，该奖项是根据持续创新软件基础设施征集的建议而设立的。 该奖项支持开发一套新的软件工具，用于计算生物分子自由能，过渡路径和反应速率，这些工具将基于并增强PI的ABMD/REMD/SMD代码套件。新的功能将被添加到现有的代码，这将大大提高软件的适用性，具有挑战性的生物分子问题。具体而言，PI旨在实施和开发：（一）处理动态耦合的多个步行者或副本以增强采样的能力;（二）引入过渡路径理论和采样方法，用于计算反应速率和相关物理量;以及（iii）引入“弦方法”，三维自由能计算和重要的最小自由能路径的计算。这些软件工具将在开源GPL下发布，并作为AMBER软件包的一部分发布。为了测试和展示软件包的工作原理，PI们将把这些方法应用于手性变化起重要作用的生物分子系统，包括：富含脯氨酸的系统，主要是胶原蛋白和一类新的细胞穿透肽，以及B和Z双螺旋中的DNA和RNA。该奖项还将通过以下方式加强教育：少数民族学生的辅导和招聘，生物物理学选项的发展，研究课题融入当前的教育论坛，与当地学校合作，以及一个新的计算科学与工程研究所的发展。非技术总结网络基础设施办公室，材料研究部，化学部，土木，机械，和制造业创新为该奖项提供资金，该奖项是根据持续创新软件基础设施征集的建议而设立的。 该奖项支持开发一套新的软件工具，以计算涉及生物分子的化学反应速率。这些代码还将能够计算在生化系统中可以转化为有用功的能量。这些代码将通过一个广泛使用的软件包AMBER分发，该软件包有助于计算化学，生物化学，化学工程，材料和生物物理社区的软件网络基础设施。它将使涉及生物分子的广泛计算研究成为可能。可能的应用包括研究生物分子的结构和转化，提供有关其可能功能的信息，模拟抗生素和模拟纳米级技术应用。该奖项还将通过以下方式加强教育：指导和招募少数民族学生，开发生物物理学选项，将研究主题纳入当前的教育论坛，与当地学校合作，以及开发新的计算科学与工程研究所。