PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDS

整个PHENIX项目旨在创建一个快速开发新方法的综合平台 自动结构解决方案，导致软件系统可以从实验x射线衍射 数据一直到最小偏差的最终模型。结构验证(评估全局和局部准确性 分子模型)是这一过程的必要部分。更重要的是，如果验证标准 可在PHENIX系统中使用，它们可以帮助改进整个 进程。杜克大学的团队开发了运动学图形，开创了全原子接触分析的先河 独立验证信息的新来源，为RNA引入了新的验证标准，以及 大大更新了蛋白质的传统构象标准。这使得MolProbity网站 服务和相关软件：可用于诊断和实际纠正的最完整的系统 大分子模型中的问题，这些方法非常适合于在 凤凰城。项目V将合作实现以下研究目标：a)提供全原子接触， PHENIX内的几何和其他质量标准，既针对用户的高级别，也包括低级别的AS 其他软件组件可直接访问的功能；b)用于核酸工具开发， 贡献经过质量过滤的片段文库、RNA主干旋转体、构象推断 最佳确定的地图特征和新的验证措施；c)为了精化和模型完成， 开发基于自动化的MolProbity结构校正、氢的精炼的新策略 原子接触和旋转体集合模型的构建；d)开发定制的3D和2D运动学 图形显示整个PHENIX过程中选定阶段的结果和备选方案。

The overall PHENIX project seeks to create an integrated platform for rapid development of new methods in automated structure solution, resulting in a software system that can go from experimental x-ray diffraction data all the way to a minimally biased final model. Structure validation (evaluating global and local accuracy of the molecular model) is a required part of such a process. Even more importantly, if the validation criteria are available within the PHENIX system, they can help improve automated decision-making throughout the process. The Duke group developed kinemage graphics, pioneered all-atom contact analysis as a powerful new source of independent validation information, introduced new validation criteria for RNA, and significantly updated the traditional conformational criteria for proteins. This makes the MolProbity web service and related software the most complete system available for diagnosing and then actually correcting problems in macromolecular models, and these methods are well-suited to adaptation and automation within PHENIX. Project V will collaboratively pursue the following research aims: a) provide all-atom contact, geometrical, and other quality criteria within PHENIX, both at a high level for users and at a low level as functions directly accessible by the other software components; b) for the nucleic-acid tool development, contribute quality-filtered fragment libraries, RNA backbone rotamers, conformational inference from the best-determined map features, and new validation measures; c) for refinement and model completion, develop new strategies based on automation of MolProbity structure corrections, refinement of hydrogen atom contacts, and construction of rotameric-ensemble models; d) develop custom 3D and 2D kinemage graphics to display results and alternatives at chosen stages throughout the PHENIX process.