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，用于快速开发新方法 自动化结构解决方案，产生可从实验 X 射线衍射中得出的软件系统 数据一直到偏差最小的最终模型。结构验证（评估全局和局部精度 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 在 PHENIX 系统中可用，它们可以帮助改进整个过程中的自动化决策 过程。杜克大学团队开发了 kinemage 图形，开创了全原子接触分析作为强大的 独立验证信息的新来源，引入了新的 RNA 验证标准，以及 显着更新了蛋白质的传统构象标准。这使得 MolProbity 网络 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内部的适应和自动化 凤凰。项目 V 将共同追求以下研究目标：a) 提供全原子接触， PHENIX 中的几何和其他质量标准，无论是对用户而言的高水平还是对用户而言的低水平 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库、RNA主链旋转异构体、构象推断 最佳确定的地图特征和新的验证措施； c) 用于细化和模型完成， 开发基于 MolProbity 结构校正自动化、氢精炼的新策略 原子接触和旋转异构系综模型的构建； d) 开发定制 3D 和 2D 运动图像 图形显示整个 PHENIX 流程中选定阶段的结果和替代方案。