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.

摘要/摘要 我的实验室的Molprobity Web服务用于诊断和指导对本地建模错误的纠正 大分子晶体结构已被证明非常有效，并且大多数研究都使用 全球社区。但是，由于最近对可以扩展的新方法产生了迫切需求 在2.5-4Å范围内，Molprobity达到了较差的分辨率。这适用于令人兴奋的大分子 机器“通过晶体学解决，尤其是“高分辨率”冷冻结构的激增 自从检测器和图像收集技术革命以来，现在可以访问。由于几个原因，我们的 现有的诊断标准（以及其他所有人）在没有肽方向的分辨率上分解 在地图密度中可见较长。我们已经开发了一个名为Cablam的新工具，该工具的长度是多余的 规模，这在我们对Cryoem模型挑战的评估中被证明非常有效。那 经验还为我们提供了其他几个标准的想法，这些标准可能诊断出2.5-4Å常见的错误， 例如翻转的胡椒粉和局部序列未对准。该建议旨在创建一个统一的 这些解决方案的工具包在莫尔普利上，这是一种急需的功能，目前不存在 任何地方。这些新结构在生物医学上的重要性越重要，不是建模就越重要 催化剂，动力学，药物设计或其他特定结合的关键部位的错误氨基酸。 在开发原始霉菌网站时，我们发现这种新工具永远不会充当一个 期望，并且需要进行实际的多种生产使用，因此需要进行广泛的测试。对于这个建议，我们将 通过称为“宝石”的工作流程，使这些测试立即对结构的最终用户有价值。我们 将识别单独的X射线或冷冻结构，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本地失误。如果记录员愿意， 我们将使用新工具协作治愈这些问题。今年的重要变化 促进此目标是WWPDB正在实现档案版本系统以启用坐标 更新而无需更改PDB代码，这使结构生物学家更愿意存入 校正的宝石结构。创建这些宝石的教训将是调整新的主要指南 工具包，以最大程度的有效性，易用性和在较低分辨率下的最小虚假更改。 现在，对Molprobity提供向开放的复杂，动态服务的能力有了新的威胁 在越来越敌对的互联网环境中，全球科学界。最近有或越酸 是极其复杂的攻击的目标，这需要非常重要的人员努力 包括近恒定监控，恢复和与医疗中心安全的密切合作 专家。我们已经插入了一些漏洞，但是需要更多的工作，例如我们当前的补丁 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。