Integrated resource for reproducibility in macromolecular crystallography

大分子晶体学重现性的综合资源

• 批准号: 9280987
• 负责人: WLADEK MINOR
• 金额: $ 47.19万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-06-01 至 2019-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9280987
• 关键词: Address; Algorithmic Analysis; Algorithmic Software; Algorithms; Archives; Biological; Calibration; Collection; Communities; Computer software; Crystallography; Data; Data Analyses; Data Collection; Data Set; Databases; Deposition; Detection; Development; Diffuse; Discipline; Disease; Educational workshop; Ensure; Fraud; Goals; Head; Ice; Image; Image Analysis; Infection; Learning; Libraries; Life; Ligands; Link; Location; Metadata; Methods; Microscopic; Modeling; Molecular; Morphologic artifacts; Network-based; Online Systems; Procedures; Process; Proteins; Protocols documentation; Readability; Reproducibility; Research; Research Personnel; Resolution; Resources; Roentgen Rays; Semantics; Site; Software Tools; Standardization; Structural Biologist; Structure; Synchrotrons; System; Technology; Technology Transfer; Testing; Training; Twin Multiple Birth; Validation; Vendor; Work; X-Ray Crystallography; beamline; beneficiary; cell dimension; data mining; data reduction; data wrangling; density; design; detector; electron density; experimental study; geometric methodologies; heuristics; imaging program; improved; member; prevent; programs; public health relevance; repository; statistics; structural biology; structural genomics; syntax; three dimensional structure; tool; tool development; working group

 DESCRIPTION (provided by applicant): We propose the development of a collection of data wrangling tools to store, parse, manipulate, validate, curate, analyze, and disseminate macromolecular diffraction images together with all associated relevant metadata. The proposed system will have several benefits, by (1) creating a means to improve existing structures as technology for processing diffraction image advances, (2) detecting errors (and potentially, fraud) in existing structures to ensure structure quality and reproducibility, (3) preventing the loss of data collected by structural genomics and other programs that have closed or will close, (4) providing data for analysis of diffuse diffraction effects, and (5) buildng a "training set" for new diffraction analysis algorithms and hardware. Biologists, bioinformaticians, and software and hardware developers will all be beneficiaries of these tools. The proposed research is designed for semantic rather than syntactic analysis of diffraction images, and has several specific goals. First, we will develop tools for automatically extracting and curating diffraction images and associated metadata, as well as producing descriptions of all data needed for reprocessing when methods for structure determination improve. Second, we will create a web-based system for organizing, searching, analyzing, and data mining of appropriate subsets of diffraction images and associated metadata in machine- readable formats. This will include a comprehensive API for programmatic access, the ability to link multiple instances into a distributed federation, and state-of-the-art compression and transfer technologies. Third, we will develop tools to automatically validate, preprocess, and score diffraction images, and to detect potential issues and errors. These tools will make use of new and existing programs for image and data analysis, contain heuristics to identify possible errors, and provide statistics to correlate errors with specific metadata. Fourth, we will create a mechanism to discover diffraction data that have not yielded X-ray structures with currently available methods. Fifth, we will set up a pilot resource incorporating all the developed tools, and collect a test data set for the development of new tools for validation and error detection. We will work closely with multiple collaborators. Most important is the RCSB Protein Data Bank (PDB), who will help us ensure the accuracy and completeness of the diffraction metadata. Other partners will include the diffuse X-ray scattering community, detector vendors, synchrotron beamline managers, members of the IUCr Diffraction Data Deposition Working Group (DDDWG) and the crystallographic community in general. Together with the RCSB PDB, we will organize workshop(s) with these communities in order to (a) improve metadata extraction and (b) better define subsets of diffraction images. By addressing the currently common, irreversible and unnecessary loss of raw diffraction data during the data reduction process, our project helps ensure that the discipline of macromolecular crystallography is capable of continuous self-improvement.

 描述（由适用提供）：我们建议开发一系列数据包装工具，用于存储，解析，操纵，验证，策划，策展人，分析和分发大分子分子衍射图像以及所有相关的相关元数据。 The proposed system will have several benefits, by (1) creating a means to improve existing structures as technology for processing diffraction image advances, (2) detecting errors (and potentially, fraud) in existing structures to Ensure structure quality and reproducibility, (3) preventing the loss of data collected by structural genomics and other programs that have closed or will close, (4) providing data for analysis of diffuse diffraction effects, and (5) buildng a "training设置“用于新的衍射分析算法和硬件。生物学家，生物信息学家， 软件和硬件开发人员将对这些工具的所有收益。拟议的研究设计用于衍射图像的语义而不是句法分析，并且具有多个特定目标。首先，我们将开发用于自动提取和策划衍射图像和相关元数据的工具，并在结构确定方法改善时对重新处理所需的所有数据进行描述。其次，我们将创建一个基于Web的系统，用于组织，搜索，分析和数据挖掘衍射图像的适当子集和机器可读格式中相关的元数据。这将包括用于程序化访问的全面API，将多个实例链接到分布式联合会以及最新的压缩和转移技术的能力。第三，我们将开发自动验证，预处理和评分衍射图像并检测潜在问题和错误的工具。这些工具将利用新的和现有的程序进行图像和数据分析，包含启发式方法以识别可能的错误，并提供统计信息以将错误与特定的元数据相关联。第四，我们将创建一种机制，以发现尚未产生X射线结构的衍射数据。第五，我们 将设置一个编码所有开发工具的飞行员资源，并为 开发用于验证和错误检测的新工具。我们将与多个合作者紧密合作。最重要的是RCSB蛋白数据库（PDB），他们将帮助我们确保衍射元数据的准确性和完整性。其他合作伙伴将包括弥漫性X射线散射社区，检测器供应商，同步梁线经理，IUCR衍射数据沉积工作组（DDDWG）的成员以及一般的晶体学界。与RCSB PDB一起，我们将与这些社区一起组织研讨会，以（a）改善元数据提取，（b）更好地定义衍射图像的子集。通过解决当前常见的，不可逆的和不必要的原始衍射数据丢失，我们的项目有助于确保大分子晶体学的学科能够连续自我提高。

项目成果

CheckMyMetal: a macromolecular metal-binding validation tool.

• DOI: 10.1107/s2059798317001061
• 发表时间: 2017-03-01
• 期刊: Acta crystallographica. Section D, Structural biology
• 作者: Zheng H;Cooper DR;Porebski PJ;Shabalin IG;Handing KB;Minor W
• 通讯作者: Minor W

Detect, correct, retract: How to manage incorrect structural models.

• DOI: 10.1111/febs.14320
• 发表时间: 2018-03
• 期刊: The FEBS journal
• 作者: Wlodawer A;Dauter Z;Porebski PJ;Minor W;Stanfield R;Jaskolski M;Pozharski E;Weichenberger CX;Rupp B
• 通讯作者: Rupp B

Characterizing metal-binding sites in proteins with X-ray crystallography.

• DOI: 10.1038/nprot.2018.018
• 发表时间: 2018-05
• 期刊: Nature protocols
• 影响因子: 14.8
• 作者: Handing KB;Niedzialkowska E;Shabalin IG;Kuhn ML;Zheng H;Minor W
• 通讯作者: Minor W

A close look onto structural models and primary ligands of metallo-β-lactamases.

• DOI: 10.1016/j.drup.2018.08.001
• 发表时间: 2018-09
• 期刊: Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy
• 作者: Raczynska JE;Shabalin IG;Minor W;Wlodawer A;Jaskolski M
• 通讯作者: Jaskolski M

Correcting the record of structural publications requires joint effort of the community and journal editors.

• DOI: 10.1111/febs.13765
• 发表时间: 2016-12
• 期刊: The FEBS journal
• 作者: Rupp B;Wlodawer A;Minor W;Helliwell JR;Jaskolski M
• 通讯作者: Jaskolski M