MolProbity Validation & Corrections: for Crystallography, PDB & Biomedicine

摩尔概率验证

• 批准号: 8077177
• 负责人: DAVID Claude RICHARDSON
• 金额: $ 32.91万
• 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/8077177
• 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; 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验证和校正：用于晶体学、PDB和生物医学”总结：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接受为改进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，这些错误会损害解释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。这种复杂且使用量很大的Web服务需要不断提升效率和良好实践，以保持透明、简单和可靠的使用，以满足现在依赖它的快速增长的用户群。不久，在wwPDB验证工作组推荐的新标准中，将需要在全球范围内使用MolProbity输出。需要进一步的自动化来进行误差校正，包括全原子接触，在结构解决方案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，这些实验室偶尔进行晶体结构，以支持他们的主要生物和生物医学工作。当前关于在较低分辨率下提高准确性的方法和对于大蛋白质/核酸复合物的方法的研究应该成为MolProbity的一部分，沿着是在非常高的分辨率下更好地处理多种构象，重新检查基础参数，以及为NMR、预测和模拟用途定制的附加功能。 更广泛地实施MolProbity校正将通过提高结构的整体准确性来帮助所有最终用户，而简单的MolProbity验证有助于最终用户评估与其工作直接相关的局部区域的结构细节的可靠性。这个提议的一个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MolProbit风格的校正，使我们自己退出业务。) 公共卫生相关性：MolProbity是一个用于结构验证和校正的Web服务。这种方法的使用已经提高了生物学和医学上重要的大分子结构的准确性，如全球PDB数据库的统计数据所示。我们寻求增加MolProbity的易用性，有效性和范围，并将其标准整合到结构测定的标准程序中，以利于结构生物学家，数据库和生物医学最终用户。)