EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):28-39. doi: 10.1109/TCBB.2007.1003.


Cryo-EM has become an increasingly powerful technique for elucidating the structure, dynamics, and function of large flexible macromolecule assemblies that cannot be determined at atomic resolution. However, due to the relatively low resolution of cryo-EM data, a major challenge is to identify components of complexes appearing in cryo-EM maps. Here, we describe EMatch, a novel integrated approach for recognizing structural homologues of protein domains present in a 6-10 A resolution cryo-EM map and constructing a quasi-atomic structural model of their assembly. The method is highly efficient and has been successfully validated on various simulated data. The strength of the method is demonstrated by a domain assembly of an experimental cryo-EM map of native GroEL at 6 A resolution.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptor Protein Complex 2 / chemistry
  • Adaptor Protein Complex 2 / ultrastructure
  • Algorithms
  • Chaperonin 60 / chemistry
  • Chaperonin 60 / ultrastructure
  • Computational Biology / methods*
  • Cryoelectron Microscopy / methods*
  • Databases, Protein
  • Image Processing, Computer-Assisted / methods*
  • Models, Molecular
  • Photosynthetic Reaction Center Complex Proteins / chemistry
  • Photosynthetic Reaction Center Complex Proteins / ultrastructure
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Structural Homology, Protein
  • Triose-Phosphate Isomerase / chemistry
  • Triose-Phosphate Isomerase / ultrastructure


  • Adaptor Protein Complex 2
  • Chaperonin 60
  • Photosynthetic Reaction Center Complex Proteins
  • Triose-Phosphate Isomerase