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

项目 5 - DUKE - 蛋白质和核酸的结构验证和改进

• 批准号: 7208315
• 负责人: JANE Shelby RICHARDSON
• 金额: $ 12.05万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7208315
• 关键词: X ray crystallography; bioengineering /biomedical engineering; biomedical automation; computer graphics /printing; computer program /software; conformation; functional /structural genomics; mathematical model; model design /development; molecular biology information system; nucleic acid structure; protein structure function; structural biology

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.

整个Phenix项目旨在创建一个集成平台，以快速开发新方法 自动结构解决方案，导致可以从实验X射线衍射进行的软件系统 数据一直到最小偏见的最终模型。结构验证（评估全球和本地准确性 分子模型）是这种过程的必需部分。更重要的是，如果验证标准 可在Phenix系统中可用，它们可以帮助改善整个过程中的自动决策 过程。杜克集团开发了Kinemage图形，开创了全部原子接触分析作为强大的 独立验证信息的新来源，引入了RNA的新验证标准，以及 显着更新了蛋白质的传统构象标准。这使Molprobity网络 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，这些方法非常适合适应和自动化 凤凰。项目V将协作追求以下研究目的：a）提供全部原子联系， 卑鄙的用户和低水平的几何和其他质量标准，均为低水平 其他软件组件可以直接访问功能； b）对于核酸工具的发展， 贡献质量过滤的片段，RNA骨架旋转植物，构象推断 最确定的地图功能和新的验证措施； c）用于改进和模型完成， 基于霉菌结构校正的自动化，氢化的改进，制定新策略 原子触点和旋转构造模型的构建； D）开发自定义3D和2D Kinemage 在整个Phenix过程中，在所选阶段显示结果和替代方案的图形。