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.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 MODELLER是一个软件包，用于蛋白质和复合物的比较建模，在Sali实验室开发和维护。它还被用作大量实验室项目的基础，如MODBASE和MODPIPE，并免费提供给学术使用。MODELLER的几个重要模块的Web接口，如比较建模本身，对齐工具或从头循环细化，也在开发中。我们的愿望是使MODELLER易于使用，快速，灵活，足以应用于新的问题，如对接比较模型。我们希望在用户使用的平台上提供MODELLER，例如Alpha;因此，socrates将偶尔用于编译，基准测试和测试MODELLER的Alpha版本。此外，为了便于使用和提高互操作性，正在将MODELLER从一个单一的FORTRAN应用程序转换为一组Python和C模块，以使用标准文件格式和表示进行比较建模。MODELLER与其他基于Python的软件包（如CGL自己的Chimera软件）之间的集成将在这些系统上进行测试。