IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
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Abstract

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.

Abstract Image

Abstract Image

IHMCIF:整合结构确定方法的 PDBx/mmCIF 数据标准扩展。
IHMCIF(github.com/ihmwg/IHMCIF)是一个数据信息框架,支持归档和传播通过整合或混合建模(IHM)确定的大分子结构,并使其具有可查找性、可访问性、可互操作性和可重用性(FAIR)。IHMCIF 是蛋白质数据库交换/大分子晶体学信息框架(PDBx/mmCIF)的扩展,该框架是蛋白质数据库(PDB)的框架,用于归档通过实验确定的生物大分子结构及其相互之间的复合物和小分子配体(如酶辅因子和药物)的原子结构。IHMCIF 是 PDB-Dev 原型系统的基础数据标准,用于归档和传播综合结构。它采用灵活的数据表示方式来描述跨越多个时空尺度和结构状态的整合结构,并定义了各种实验方法对整合结构生物学的限制。全球蛋白质数据库(wwPDB)整合或混合方法工作组(wwpdb.org/task/hybrid)收集了大量的社区意见和建议,IHMCIF扩展就是在这些意见和建议的基础上创建的。在此,我们将介绍 IHMCIF 的发展情况,以支持不断发展的方法和整合结构生物学的持续进步。最终,IHMCIF 将促进 PDB-Dev 数据和工具与 PDB 存档的统一,从而使整合结构可以通过 PDB 存档和传播。
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来源期刊
Journal of Molecular Biology
Journal of Molecular Biology 生物-生化与分子生物学
CiteScore
11.30
自引率
1.80%
发文量
412
审稿时长
28 days
期刊介绍: Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.
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