ArticleBioinformatics (Oxford, England)2016
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Structure first - exploration and discovery with cryo-electron microscopy.Journal of cell science · 2026Review
- Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.Journal of molecular biology · 2025Article
- Protein identification using Cryo-EM and artificial intelligence guides improved sample purification.Journal of structural biology: X · 2025Article
- CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features.Bioinformatics (Oxford, England) · 2025Article
- Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.Protein science : a publication of the Protein Society · 2025Article
- FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.Genomics, proteomics & bioinformatics · 2024Article
- Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features.Nature communications · 2024Article
- Structural Outlier Detection and Zernike-Canterakis Moments for Molecular Surface Meshes-Fast Implementation in Python.Molecules (Basel, Switzerland) · 2023Article
- Csx28 is a membrane pore that enhances CRISPR-Cas13b-dependent antiphage defense.Science (New York, N.Y.) · 2023Article
- Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday.Biophysical reviews · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology.European journal of microbiology & immunology · 2022Review
- 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
- VESPER: global and local cryo-EM map alignment using local density vectors.Nature communications · 2021Article
- Simplified geometric representations of protein structures identify complementary interaction interfaces.Proteins · 2021Article
- TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D.Nucleic acids research · 2020Article
- Real time structural search of the Protein Data Bank.PLoS computational biology · 2020Article
- Searching for 3D structural models from a library of biological shapes using a few 2D experimental images.BMC bioinformatics · 2018Article
- The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization.Cell surface (Amsterdam, Netherlands) · 2018Article
- New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).Protein science : a publication of the Protein Society · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledOmokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB). The server compares global shapes of assemblies independent of sequence order and number of subunits. As a search query, the user inputs a structure ID (PDB ID or EMDB ID) or uploads an atomic model or 3D density map to the server. The search is performed usually within 1 min, using one-dimensional profiles (incremental distance rank profiles) to characterize the shapes. Using the gmfit (Gaussian mixture model fitting) program, the found structures are fitted onto the query structure and their superimposed structures are displayed on the Web browser. Our service provides new structural perspectives to life science researchers. AVAILABILITY AND IMPLEMENTATION: Omokage search is freely accessible at http://pdbj.org/omokage/.
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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.