Extending MolProbity Diagnosis & Healing Methods to Empower Better CryoEM & Xray Models at 2.5-4A Resolution, plus Versioned, Redeposited "GEMS" for Important Individual Structures

扩展 MolProbity 诊断

• 批准号: 10414895
• 负责人: DAVID Claude RICHARDSON
• 金额: $ 41.42万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10414895
• 关键词: Affect; Amino Acids; Archives; Binding; Biological; Catalysis; Code; Collaborations; Collection; Communities; Complex; Cryoelectron Microscopy; Crystallization; Crystallography; Databases; Deposition; Diagnosis; Diagnostic Errors; Diagnostic Services; Drug Design; Effectiveness; Environment; Goals; Human Resources; Image; Individual; Instruction; Internet; Length; Maps; Medical; Medical center; Methods; Modality; Modeling; Molecular Machines; Monitor; Peptides; Production; Proteins; Research; Resolution; Roentgen Rays; Security; Services; Site; Structural Biologist; Structure; System; Technology; Testing; Update; Validation; Work; density; detector; diagnostic criteria; experience; healing; improved; nucleic acid structure; public health relevance; tool; web services

Summary/Abstract My lab's MolProbity web service for diagnosing and guiding correction of local modeling errors in macromolecular crystal structures has proven highly effective and is used by most of that research community worldwide. However, as urgent need has recently arisen for new methods that can extend MolProbity's reach to poorer resolutions in the 2.5-4Å range. That applies to the exciting, big "molecular machines" solved by crystallography, and especially to the surge of "high resolution" cryoEM structures now accessible since the revolution in detector and image collection technology. For several reasons, our existing diagnostic criteria (and everyone else's) break down at resolutions where peptide orientation is no longer visible in the map density. We have developed a new tool called CaBLAM at a multi-residue length scale, which proved extremely effective in our assessments for the CryoEM Model Challenge. That experience also gave us ideas for several other criteria that could diagnose errors common at 2.5-4Å, such as flipped-over peptides and local sequence misalignments. This proposal aims to create a unified toolkit for these resolutions in MolProbity, an urgently needed functionality which does not currently exist anywhere. The more biomedically important these new structures are, the more crucial it is not to model the wrong amino acid at the critical site for catalysis, dynamics, drug design, or other specific binding. When developing the original MolProbity site we found that such new tools never act quite as one expects, and so extensive testing in real, varied production use is necessary. For this proposal, we will make those tests immediately valuable to the end-users of structures by a workflow called "GEMS". We will identify individual x-ray or cryoEM structures that are a most-used archetype for their molecule but which contain local misfittings that affect their functional interpretation. If the depositor-of-record is willing, we will collaborate on healing those problems using the new tools. An important change this year to facilitate this goal is that the wwPDB is implementing an archival versioning system to enable coordinate updates without changing the PDB code, which makes structural biologists much more willing to deposit a corrected GEM structure. The lessons from creating these GEMS will be a major guide in tuning the new toolkit for maximum effectiveness, ease of use, and a minimum of false changes at the lower resolutions. There is now a new threat to MolProbity's ability to provide complex, dynamic services open to the worldwide scientific community in an increasingly hostile internet environment. MolProbity has recently been the target of extremely sophisticated attacks, which have required very significant personnel effort including near-constant monitoring, reinstallations, and close collaboration with medical center security experts. We have plugged some vulnerabilities but more work is needed, such as patches to our current version, perhaps a new web deployment modality, and laying the groundwork for a major redesign.

总结/摘要 我的实验室的MolProbity Web服务，用于诊断和指导纠正本地建模错误， 大分子晶体结构已被证明是非常有效的，并被大多数研究所使用 世界各地的社区。然而，由于迫切需要最近出现的新方法， MolProbity的分辨率在2.5- 4 μ m范围内较差。这适用于令人兴奋的，大的“分子 晶体学解决的“机器”，特别是“高分辨率”cryoEM结构的激增 自从探测器和图像收集技术革命以来，现在可以使用。出于几个原因，我们 现有的诊断标准（以及其他人的）在肽方向不确定的分辨率上失败了。 在地图密度中可见时间更长。我们已经开发了一种新的工具，称为CaBLAM在多残基长度 规模，这在我们的CryoEM模型挑战的评估中被证明是非常有效的。的 经验还为我们提供了其他几个可以诊断2.5- 4GHz常见错误的标准， 例如翻转肽和局部序列错配。该提案旨在建立统一的 MolProbity中这些决议的工具包，这是一个迫切需要的功能，目前还不存在 anywhere.这些新的结构在生物医学上越重要，就越不需要建模 在催化、动力学、药物设计或其他特异性结合的关键位点上的错误氨基酸。 在开发最初的MolProbity网站时，我们发现这些新工具从来没有像一个一样运行 因此，在真实的、不同的生产使用中进行广泛的测试是必要的。对于这一建议，我们将 通过称为“GEMS”的工作流程，使这些测试对结构的最终用户立即有价值。我们 将识别单个X射线或cryoEM结构，这些结构是其分子最常用的原型， 其包含影响其功能解释的局部失配。如果档案保管人愿意， 我们将合作使用新工具来解决这些问题。今年的一个重要变化是， 促进实现这一目标的一个因素是，wwPDB正在实施一个档案版本管理系统，以使协调 更新，而不改变PDB代码，这使得结构生物学家更愿意存款， 修正GEM结构。创建这些GEMS的经验教训将是调整新的 最大的有效性，易用性，并在较低的分辨率最小的错误变化的工具包。 现在，MolProbity向用户提供复杂、动态服务的能力面临新的威胁 在日益恶劣的互联网环境下，全球科学界。MolProbity最近 成为极其复杂的攻击的目标，这需要非常大的人员努力 包括近乎持续的监控、重新安装以及与医疗中心安全部门的密切合作 专家我们已经修补了一些漏洞，但还需要做更多的工作，例如为我们当前的 版本，也许是一个新的Web部署模式，并为重大的重新设计奠定基础。