ArticleNucleic acids research2012
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- Accurate SPARQL generation via in-context learning and schema-based query construction.Bioinformatics (Oxford, England) · 2026Article
- Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.Journal of molecular biology · 2025Article
- Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.Protein science : a publication of the Protein Society · 2025Article
- Article
- Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method.Scientific data · 2024Article
- PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.Database : the journal of biological databases and curation · 2024Article
- PDBms-An online tool for PDB file splitting and interactive molecular visualization.Interdisciplinary sciences, computational life sciences · 2023Article
- Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network.Biomolecules · 2023Article
- Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday.Biophysical reviews · 2022Article
- Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.Biophysical reviews · 2022Review
- Some reflections on a career in science and a note of thanks to the contributors of this Special Issue.Biophysical reviews · 2022Article
- Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network.Biomolecules · 2022Article
- Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin.Life (Basel, Switzerland) · 2022Article
- Computational Study on the Dynamics of Mycobacterium Tuberculosis RNA Polymerase Assembly.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.Protein science : a publication of the Protein Society · 2022Article
- The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science.RSC advances · 2021Review
- The Protein Data Bank Archive.Methods in molecular biology (Clifton, N.J.) · 2021Review
- PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins.Database : the journal of biological databases and curation · 2020Article
- IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites.Genomics, proteomics & bioinformatics · 2020Article
- BioHackathon 2015: Semantics of data for life sciences and reproducible research.F1000Research · 2020Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.