Situs: A package for docking crystal structures into low-resolution maps from electron microscopy

J Struct Biol. Apr-May 1999;125(2-3):185-95. doi: 10.1006/jsbi.1998.4080.


Three-dimensional image reconstructions of large-scale protein aggregates are routinely determined by electron microscopy (EM). We combine low-resolution EM data with high-resolution structures of proteins determined by x-ray crystallography. A set of visualization and analysis procedures, termed the Situs package, has been developed to provide an efficient and robust method for the localization of protein subunits in low-resolution data. Topology-representing neural networks are employed to vector-quantize and to correlate features within the structural data sets. Microtubules decorated with kinesin-related ncd motors are used as model aggregates to demonstrate the utility of this package of routines. The precision of the docking has allowed for the extraction of unique conformations of the macromolecules and is limited only by the reliability of the underlying structural data.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Computer Graphics
  • Computer Simulation*
  • Crystallography, X-Ray*
  • Drosophila Proteins*
  • Kinesin / ultrastructure
  • Macromolecular Substances
  • Microscopy, Electron*
  • Microtubules / ultrastructure
  • Models, Molecular*
  • Molecular Motor Proteins / ultrastructure
  • Neural Networks, Computer
  • Protein Conformation*
  • Software*
  • User-Computer Interface


  • Drosophila Proteins
  • Macromolecular Substances
  • Molecular Motor Proteins
  • ncd protein, Drosophila
  • Kinesin