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Real Time Structural Search of the PDB

08/11

A new paper describes a novel method that detects similarity between protein shapes and that works equally fast for any size of proteins or assemblies.

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

This method drives the Structure Similarity option in Advanced Search.

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The system attempts to assess global 3D-shape similarity by using BioZernike descriptors that capture the global volumetric shape of the protein. 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

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