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 我的实验室的MolProbity Web服务，用于诊断和指导 大分子晶体结构已被证明是非常有效的，并被大多数研究使用 世界各地的社区。然而，由于最近出现了对可扩展新方法的迫切需求 MolProbity的分辨率在2.5-4？范围内较差。这适用于令人兴奋的大分子 结晶学所解决的“机器”问题，尤其是“高分辨率”低温电磁结构的激增 自从探测器和图像采集技术革命以来，现在可以访问。出于几个原因，我们的 现有的诊断标准(和其他所有人的标准)在多肽取向为NO的分辨率下会崩溃 在贴图密度中不再可见。我们已经开发了一种名为CaBLAM的多残基长度的新工具 这在我们对低温EM模型挑战的评估中被证明是非常有效的。那 经验还给了我们一些其他标准的想法，这些标准可以诊断2.5-4？常见的错误， 例如翻转的多肽和局部序列错位。这项提案旨在创建一个统一的 MolProbity中用于这些分辨率的工具包，这是目前尚不存在的迫切需要的功能 随便哪都行。这些新结构在生物医学上越重要，就越不需要对其进行建模 在催化、动力学、药物设计或其他特定结合的关键位置有错误的氨基酸。 在开发最初的MolProbity站点时，我们发现这样的新工具从来都不能起到完全相同的作用 因此，在实际的、各种生产用途中进行广泛的测试是必要的。对于这项提议，我们将 通过一种称为“宝石”的工作流程，使这些测试对结构的最终用户立即具有价值。我们 将识别作为其分子最常用原型的单个X射线或低温电子显微镜结构，但 它们包含影响其功能解释的局部不匹配。如果登记的存款人愿意， 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 促成这一目标的是，WWPDB正在实施档案版本化系统，以实现协调 更新而不更改PDB代码，这使得结构生物学家更愿意在 修正了宝石结构。创建这些宝石的经验教训将成为调整新版本的主要指南 工具包，最大限度地提高效率、易用性，并在较低分辨率下最大限度地减少错误更改。 现在，MolProbity提供复杂、动态的服务的能力受到了新的威胁 在日益充满敌意的互联网环境中，世界科学界。MolProbity最近 是极其复杂的袭击的目标，这需要非常大量的人员努力 包括近乎不间断的监控、重新安装以及与医疗中心安全部门的密切协作 专家。我们已经填补了一些漏洞，但还需要做更多的工作，例如为我们当前的 版本，也许是一种新的网络部署模式，并为重大的重新设计奠定了基础。