ArticleNucleic acids research2017
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- TogoMCP: natural language querying of life-science knowledge graphs via schema-guided LLMs and the Model Context Protocol.Database : the journal of biological databases and curation · 2026Article
- Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.Journal of molecular biology · 2025Article
- Familial Episodic Pain Syndrome: A Japanese Family Harboring the Novel Variant c.2431C>T (p.Leu811Phe) in SCN11A.Biochemical genetics · 2025Article
- Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.Protein science : a publication of the Protein Society · 2025Article
- CellMsg: graph convolutional networks for ligand-receptor-mediated cell-cell communication analysis.Briefings in bioinformatics · 2024Article
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- CytoSIP: an annotated structural atlas for interactions involving cytokines or cytokine receptors.Communications biology · 2024Article
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- SPTLC2 variants are associated with early-onset ALS and FTD due to aberrant sphingolipid synthesis.Annals of clinical and translational neurology · 2024Article
- Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations.ACS omega · 2024Article
- The SIB Swiss Institute of Bioinformatics Semantic Web of data.Nucleic acids research · 2024Article
- LSTM-SAGDTA: Predicting Drug-target Binding Affinity with an Attention Graph Neural Network and LSTM Approach.Current pharmaceutical design · 2024Article
- Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02.Protein science : a publication of the Protein Society · 2023Article
- Molecular docking in organic, inorganic, and hybrid systems: a tutorial review.Monatshefte fur chemie · 2023Review
- Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL.Communications biology · 2023Article
- Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking.Biophysical reviews · 2022Review
- 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
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), 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. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.
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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.