MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine

摩尔概率验证

• 批准号: 8242090
• 负责人: DAVID Claude RICHARDSON
• 金额: $ 31.44万
• 依托单位: DUKE UNIVERSITY
• 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 2015-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8242090
• 关键词: Adoption; Advisory Committees; Automation; Biochemical Reaction; Biological; Businesses; Code; Color; Communities; Complex; Computer software; Crystallography; Data; Databases; Deposition; Diagnosis; Drug Design; Educational workshop; Effectiveness; Ensure; Evaluation; Exercise; Extensible Markup Language; Future; Goals; Growth; Health; Human Biology; Hydrogen; Hydrogen Bonding; Laboratories; Length; Measures; Methodology; Modeling; Molecular Conformation; Molecular Machines; Molecular Structure; Nucleic Acids; Output; Paper; Principal Investigator; Procedures; Process; Productivity; Proteins; RNA; Radial; Reading; Recommendation; Reporting; Research; Resolution; Resources; Role; Services; Solutions; Specific qualifier value; Structural Biologist; Structure; System; Update; Validation; Water; Work; base; empowered; improved; interest; outreach; programs; public health relevance; rapid growth; restraint; simulation; software systems; statistics; success; tool; virtual; web services; web site

DESCRIPTION (provided by applicant): "MolProbity Validation and Corrections: for Crystallography, PDB, and Biomedicine" Summary: The criteria and services of our MolProbity web site and related resources have become accepted by the professional crystallography community as state-of-the-art for improving and validating structural accuracy. Macromolecular crystal structures represent extremely reliable scientific information, but they can still often contain local errors that hurt interpretation in their crucial role in applications such as understanding enzymatic reactions or molecular machines, or drug design. This complex and heavily used web service needs continued upgrading of efficiency and good practice, to maintain transparently easy and reliable use for the rapidly growing user base that now depends upon it. Differently presented MolProbity output will soon be required for worldwide PDB use in the new standards recommended by the wwPDB Validation Task Forces. Further automation is needed for error corrections incorporating all-atom contacts, application of them sooner in the structure-solution process, and integration into more of the standard software systems -- especially to help ensure reliability and productivity for the growing number of laboratories who do occasional crystal structures in support of their primary biological and biomedical work. Current research on ways of improving accuracy at lower resolutions and for large protein/nucleic acid complexes should become part of MolProbity, along with better treatment of multiple conformations at very high resolution, re-examination of underlying parameters, and additional features tailored for NMR, prediction, and simulation uses. Wider implementation of MolProbity corrections will aid all end-users of structures by improving their overall accuracy, while easy MolProbity validation helps end-users evaluate the reliability of structural details in local regions of direct relevance to their work. A goal of this proposal is essentially to put ourselves out of business by building MolProbity-style corrections into the future pipelines of structure solution and database deposition. ) PUBLIC HEALTH RELEVANCE: MolProbity is a web service for structure validation and correction. Use of this methodology is already improving accuracy of biologically and medically important macromolecular structures, as seen in statistics across the worldwide PDB database. We seek to increase MolProbity's ease, effectiveness and scope and to integrate its criteria into the standard procedures of structure determination, for the benefit of structural biologists, databases, and biomedical end-users. )

描述（由申请人提供）：“MolProbity验证和修正：用于晶体学，PDB和生物医学”摘要：我们的MolProbity网站和相关资源的标准和服务已被专业晶体学社区所接受，作为提高和验证结构准确性的最先进技术。大分子晶体结构代表了极其可靠的科学信息，但它们仍然经常包含局部错误，这损害了它们在理解酶反应或分子机器或药物设计等应用中的关键作用的解释。这种复杂且频繁使用的web服务需要不断提高效率和良好实践，以便为现在依赖它的快速增长的用户群保持透明、简单和可靠的使用。在wwPDB验证任务组推荐的新标准中，很快就需要以不同的方式呈现MolProbity输出。包括全原子接触在内的纠错需要进一步的自动化，在结构解决过程中更快地应用它们，并集成到更多的标准软件系统中——特别是为了帮助确保越来越多的实验室的可靠性和生产力，这些实验室偶尔会做晶体结构，以支持他们的主要生物学和生物医学工作。目前对提高低分辨率和大型蛋白质/核酸复合物精度的方法的研究应该成为MolProbity的一部分，同时在非常高的分辨率下更好地处理多个构象，重新检查基础参数，以及为NMR，预测和模拟用途量身定制的附加功能。MolProbity校正的广泛实施将通过提高整体精度来帮助所有结构的最终用户，而简单的MolProbity验证可以帮助最终用户评估与他们工作直接相关的局部结构细节的可靠性。这个提议的一个主要目标是通过在未来的结构解决方案和数据库沉积管道中构建molprobity风格的更正，从而使我们自己破产。)