Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB

Bioinformatics. 2016 Feb 15;32(4):619-20. doi: 10.1093/bioinformatics/btv614. Epub 2015 Oct 27.


Omokage 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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Chemical
  • Databases, Protein*
  • Internet
  • Macromolecular Substances / chemistry*
  • Microscopy, Electron*
  • Models, Molecular*
  • Normal Distribution
  • Software*


  • Macromolecular Substances