New Features

Find Similarly-Shaped Structures with Advanced Search

12/13

<I>Enter a PDB ID or URL address for a publicly-available data file (e.g., from AlphaFold, ModelArchive, ESMFold, a shared drive) to launch a Structure Similarity Search. <a href="https://url.rcsb.org/search?request=%7B%22query%22:%7B%22type%22:%22group%22,%22logical_operator%22:%22and%22,%22nodes%22:%5B%7B%22type%22:%22terminal%22,%22service%22:%22structure%22,%22parameters%22:%7B%22operator%22:%22strict_shape_match%22,%22value%22:%7B%22url%22:%22https://api.esmatlas.com/fetchPredictedStructure/MGYP000005627929.pdb%22,%22format%22:%22pdb%22%7D%7D%7D%5D%7D,%22return_type%22:%22assembly%22,%22request_options%22:%7B%22paginate%22:%7B%22start%22:0,%22rows%22:25%7D,%22results_content_type%22:%5B%22experimental%22%5D,%22sort%22:%5B%7B%22sort_by%22:%22score%22,%22direction%22:%22desc%22%7D%5D,%22scoring_strategy%22:%22combined%22%7D,%22request_info%22:%7B%22query_id%22:%22d4aba66b250c647dade9bf13869d52c6%22%7D%7D">Launch an example search that uses a Web Link</a>.</I>Enter a PDB ID or URL address for a publicly-available data file (e.g., from AlphaFold, ModelArchive, ESMFold, a shared drive) to launch a Structure Similarity Search. Launch an example search that uses a Web Link.

RCSB.org uses a novel method to quickly detect similarity between protein shapes of any size.

Use the Advanced Search>Structure Similarity option to find proteins with similar 3D protein shapes using either a PDB ID or a URL to an external structure data file (mmCIF, BinaryCIF or PDB file format).

The system attempts to assess global 3D-shape similarity by using BioZernike descriptors that capture the global volumetric shape of the protein. The search will return structures whose volumes are globally similar to the query structure provided.

Users can search for similar:

  • polymeric chains to a given chain
  • assemblies to a given assembly

Two modes of matching are available:

  • Strict: returns matches that are all relevant but may not return more distant matches
  • Relaxed: returns all similar matches, but may include some false positives

A Structure Match Score is provided in the search results when the option to return data as “Assemblies” is selected.

Advanced Search can be used to combine Structure Similarity searches with other types of queries. Visit the Advanced Search documentation to learn more.

Details about the Structure Similarity search and BioZernike descriptors have been published:

Real time structural search of the Protein Data Bank
Guzenko D, Burley SK, Duarte JM
(2020) PLoS Comput Biol 16(7): e1007970. doi: 10.1371/journal.pcbi.1007970

New Features Index