ArticleJournal of molecular biology2025
Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.
Article in Journal of molecular biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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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.
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Who cites it
13 citing papers in PubMed.
- DAQplugin: Interactive Deep Learning-Based Validation of Cryo-EM Protein Models in ChimeraX.bioRxiv : the preprint server for biology · 2026Article
- 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
- Discovery of lactylation-associated candidate hub genes and potential curcumin targets in intervertebral disc degeneration.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2026Article
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- Peptide-protein docking: from physics-based models to generative intelligence.Chemical communications (Cambridge, England) · 2026Review
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Accurate Macromolecular Complex Modeling for Cryo-EM with CryoZeta.bioRxiv : the preprint server for biology · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Molecular recognition of natural compounds by MR1 and their implication in MAIT cell activation elucidated through McMD-based dynamic docking simulations.Scientific reports · 2025Article
- Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints.Communications biology · 2025Article
- Identification of SNCA and DRD2 as key genes linking parkinson's disease and circadian rhythm through bioinformatics analysis.Scientific reports · 2025Article
- Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.Protein science : a publication of the Protein Society · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Protein Data Bank Japan (PDBj, https://pdbj.org/) is the Asian hub of three-dimensional macromolecular structure data, and a founding member of the worldwide Protein Data Bank. We have accepted, processed, and distributed experimentally determined biological macromolecular structures for over two decades. Although we collaborate with RCSB PDB and BMRB in the United States, PDBe and EMDB in Europe and recently PDBc in China for our data-in activities, we have developed our own unique services and tools for searching, exploring, visualizing, and analyzing protein structures. We have also developed novel archives for computational data and raw crystal diffraction images. Recently, we introduced the Sequence Navigator Pro service to explore proteins using experimental and computational approaches, which enables experimental structural biologists to increase their insight to help them to design their experimental studies more efficiently. In addition, we also introduced a new UniProt-integrated portal to provide users with a quick overview of their target protein and it shows a recommended structure and integrates data from various internal and external resources. With these new additions, we have enhanced our service portfolio to benefit both experimental as computational structural biologists in their search to interpret protein structures, their dynamics and function.
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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.