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

整个PHENIX项目旨在为快速开发新方法创建一个综合平台， 自动化结构解决方案，产生了一个软件系统，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（评估全局和局部精度 分子模型）是这样一个过程的必要组成部分。更重要的是，如果验证标准 在PHENIX系统中可用，它们可以帮助提高整个系统的自动化决策 过程杜克集团开发了动态图像图形，开创了全原子接触分析，作为一种强大的 新的独立验证信息来源，引入了新的RNA验证标准，以及 显著更新了蛋白质的传统构象标准。这使得MolProbity网站 服务和相关软件最完整的系统，可用于诊断，然后实际纠正 大分子模型中的问题，这些方法非常适合于适应和自动化， 菲尼克斯。项目五将共同努力实现以下研究目标：a）提供全原子接触， 几何和其他质量标准在PHENIX，无论是在高层次的用户和低层次， 可由其它软件组件直接访问的功能; B）对于核酸工具开发， 贡献质量过滤的片段文库，RNA骨架旋转异构体，构象推断， 最佳确定的地图特征，以及新的验证措施; c）对于细化和模型完善， 开发基于MolProbity结构校正自动化的新策略， 原子接触，并构建旋转系综模型; d）开发定制的3D和2D动态图像 在PHENIX流程的各个选定阶段，以图形方式显示结果和备选方案。

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.