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: 10170382
• 负责人: DAVID Claude RICHARDSON
• 金额: $ 38.94万
• 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 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10170382
• 关键词: Affect; Amino Acids; Archives; Binding; Biological; Catalysis; Code; Collaborations; Collection; Communities; Complex; Cryoelectron Microscopy; Crystallization; Crystallography; Databases; Deposition; Diagnosis; Diagnostic; 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; 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.

摘要/摘要 我实验室的 MolProbity Web 服务用于诊断和指导纠正局部建模错误 大分子晶体结构已被证明非常有效，并被大多数研究所使用 全球社区。然而，由于最近迫切需要可以扩展的新方法 MolProbity 的分辨率较低，范围为 2.5-4Å。这适用于令人兴奋的大“分子” 机器”通过晶体学解决，特别是“高分辨率”冷冻电镜结构的激增 自探测器和图像采集技术的革命以来，现在可以使用。由于多种原因，我们的 现有的诊断标准（以及其他人的）在肽方向不存在的分辨率下会崩溃 在地图密度中更清晰可见。我们开发了一种名为 CaBLAM 的新工具，具有多残基长度 事实证明，这在我们对 CryoEM 模型挑战赛的评估中非常有效。那 经验还为我们提供了一些其他标准的想法，这些标准可以诊断 2.5-4Å 常见的错误， 例如翻转肽和局部序列错位。该提案旨在建立一个统一的 MolProbity 中用于这些解决方案的工具包，这是目前不存在的迫切需要的功能 任何地方。这些新结构在生物医学上越重要，不建模就越重要 催化、动力学、药物设计或其他特异性结合的关键位点上的氨基酸错误。 在开发最初的 MolProbity 网站时，我们发现此类新工具从来没有完全发挥作用 预期，因此有必要在实际的、不同的生产用途中进行广泛的测试。对于这个提案，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产生价值。我们 将识别单个 X 射线或冷冻电镜结构，这些结构是其分子最常用的原型，但 其中包含影响其功能解释的局部失配。如果记录存款人愿意， 我们将合作使用新工具解决这些问题。今年的一个重要变化是 促进这一目标的一个原因是 wwPDB 正在实施一个档案版本控制系统，以实现协调 在不更改 PDB 代码的情况下进行更新，这使得结构生物学家更愿意存入 修正创业板结构。创建这些 GEMS 的经验教训将成为调整新系统的主要指南 工具包可实现最大的有效性、易用性，并在较低分辨率下将错误更改降至最低。 MolProbity 向公众提供复杂、动态服务的能力现在面临新的威胁。 全球科学界面临着日益敌对的互联网环境。 MolProbity 最近 是极其复杂的攻击的目标，这需要大量的人员努力 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。我们已经修复了一些漏洞，但还需要做更多工作，例如对当前的补丁进行修补 版本，也许是一种新的 Web 部署方式，并为重大重新设计奠定了基础。