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

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 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。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.