ArticleProtein science : a publication of the Protein Society2026
Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein-ligand interactions in PDB and PubChem.
Article in Protein science : a publication of the Protein Society, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed.
- Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein-ligand interactions in PDB and PubChem.Protein science : a publication of the Protein Society · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Protein Data Bank Japan (https://pdbj.org/) is the Asian hub of three-dimensional (3D) macromolecular structure data and a founding member of the global Protein Data Bank (PDB) network. Over two decades, we have curated and distributed experimentally determined structures, complementing international collaborations with Research Collaboratory for Structural Bioinformatics (RCSB) PDB, Biological Magnetic Resonance Data Bank, Protein Data Bank in Europe (PDBe), and Electron Microscopy Data Bank. In response to user demand for integrated structural and chemical data, we developed a new PubChem Portal that enables interactive exploration of compound-protein interactions. Users can view ligand binding poses in 3D via our Web Graphics Library (WebGL)-based Molmil viewer, with key interactions highlighted and key residues displayed in semi-transparent stick models, enhanced through integration with secondary databases (e.g., Dynamics DB, eF-site) for advanced insights into molecular dynamics and electrostatics. The system supports filtering by UniProt ID, Enzyme Commission (EC) number, Pfam ID, or PROSITE ID to identify structurally related compounds and visualizes protein-ligand interactions. A dynamic two-dimensional (2D) Japan Agency for Medical Research and Development representation enables real-time atom-level navigation, with clickable atoms linking to 3D structures. This tool allows users to explore compound-protein interaction landscapes, identify potential binding modes, and guide experimental design, such as mutagenesis or crystallization. The portal offers a comprehensive, user-centered ecosystem that bridges chemical and structural data, enhancing access to biological insights through integrated visualization and analysis.
Indexed as
Identifiers
What OpenQuestion holds
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.