Search NASA⌕ Search
Home/Archive/DOE OSTI

DOE OSTI · 1977324

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Westbrook, John D.·Young, Jasmine Y.·Shao, Chenghua·Feng, Zukang·Guranovic, Vladimir·Lawson, Catherine L.·Vallat, Brinda·Adams, Paul D.·Berrisford, John M.·Bricogne, Gerard·Diederichs, Kay·Joosten, Robbie P.·Keller, Peter·Moriarty, Nigel W.·Sobolev, Oleg V.·Velankar, Sameer·Vonrhein, Clemens·Waterman, David G.·Kurisu, Genji·Berman, Helen M.·Burley, Stephen K.·Peisach, Ezra
View original source ↗Read source document ↗Export metadata ↓

Abstract

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

Explore related subjects

59 BASIC BIOLOGICAL SCIENCESBiochemistry & Molecular BiologyBiological dataData managementData standardMacromolecular structureProtein data bank (PDB)

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Westbrook, John D., Young, Jasmine Y., Shao, Chenghua, Feng, Zukang, Guranovic, Vladimir, Lawson, Catherine L., Vallat, Brinda, Adams, Paul D., Berrisford, John M., Bricogne, Gerard, Diederichs, Kay, Joosten, Robbie P., Keller, Peter, Moriarty, Nigel W., Sobolev, Oleg V., Velankar, Sameer, Vonrhein, Clemens, Waterman, David G., Kurisu, Genji, Berman, Helen M., Burley, Stephen K., Peisach, Ezra. 2022-04-20. PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology. https://doi.org/10.1016/j.jmb.2022.167599

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related reports

DOE OSTI2026

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Genome-resolved insights into microbial diversity and elemental cycling in Winogradsky columns

We retained 18 MAGs with ≥50% completion and <10% contamination (i.e., at least medium quality). Of these, 10 had >90% completion and <5% contamination; however, only one (Paceibacteria Bin.003_MG) can be described as high-quality, as the others lacked a full suite of 5S, 16S, and 23S rRNA genes. To maximize the diversity of our recovered MAGs, we also retained one MAG (Chromatiaceae Bin.008_AM) with >40% (but less than 50%) completion and <5% contamination, as well as one (Rhodopseudomonas Bin.015_MK) with >90% completion and <20% (but>10%) contamination. Interestingly, significant chimerism was not detected in this MAG (40) , suggesting that the elevated contamination (20%) may instead reflect two closely related strains collapsing into a single bin. Consistent with this, contig coverage was bimodal, with roughly 17% of the assembly at ~115x and the remaining 83% at ~282x, while GC content remained uniform across both groups (~64%), arguing against contamination from a taxonomically distinct source.

59 BASIC BIOLOGICAL SCIENCES↗