DEVELOPMENT AND TESTING OF MODELLER, AND RELATED TOOLS, ON THE ALPHA PLATFORM

在 ALPHA 平台上开发和测试 MODELER 及相关工具

• 批准号: 8363599
• 负责人: ANDREJ SALI
• 金额: $ 2.24万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363599
• 关键词: Benchmarking; Chimera organism; Computer software; Development; Docking; Funding; Grant; Imagery; Informatics; Modeling; National Center for Research Resources; Principal Investigator; Pythons; Research; Research Infrastructure; Resources; Source; System; Testing; United States National Institutes of Health; Work; base; biocomputing; comparative; cost; file format; flexibility; improved; interest; interoperability; protein complex; tool; web interface

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. MODELLER is a package for comparative modeling of proteins and complexes, developed and maintained in the Sali lab. It is additionally used as the base for a large number of lab projects, such as MODBASE and MODPIPE, and is made freely available for academic use. Web interfaces to several important modules of MODELLER, such as the comparative modeling itself, alignment tools, or ab initio loop refinement, are also in development. It is our desire to make MODELLER easy to use, fast, and flexible enough to be applied to new problems, such as docking of comparative models. We wish to make MODELLER available on the platforms used by our users, such as Alpha; socrates would thus be used on an occasional basis to compile, benchmark, and test Alpha builds of MODELLER. Additionally, in the interests of ease of use and improved interoperability, work is ongoing in converting MODELLER from a monolithic FORTRAN application into a set of Python and C modules for comparative modeling, using standard file formats and representations. The integration between MODELLER and other Python-based packages, such as CGL's own Chimera software, would be tested on these systems.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 Modeller是用于在Sali Lab中开发和维护的蛋白质和复合物比较建模的软件包。它还用作大量实验室项目（例如Modbase和ModPipe）的基础，并可以自由地用于学术用途。 Web界面与建模器的几个重要模块，例如比较建模本身，对齐工具或从头开始循环的改进，也正在开发中。我们希望使建模器易于使用，快速和灵活，以便将其应用于新问题，例如比较模型对接。我们希望使Modeller在用户使用的平台上可用，例如Alpha；因此，苏格拉底将偶尔使用，以编译，基准和测试alpha构建建模器。此外，为了易于使用和提高互操作性，正在使用标准文件格式和表示形式将Modeller从单片Fortran应用程序转换为比较建模的一组Python和C模块的工作。将在这些系统上测试Modeller和其他基于Python的软件包（例如CGL自己的Chimera软件）之间的集成。