title: Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.
abstract: 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.
authors.affiliation: Department of Pharmacology, University of California, 9500 Gilman Drive, San Diego, California 92093-0365, USA. wriggers@ucsd.edu
authors.forename: W
authors.initials: W
authors.lastname: Wriggers
authors.forename: R A
authors.initials: RA
authors.lastname: Milligan
authors.forename: J A
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D000818:Animals; D003196:Computer Graphics; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D029721:Drosophila Proteins; D016547:Kinesins / Q000648:ultrastructure; D046911:Macromolecular Substances; D008854:Microscopy, Electron; D008870:Microtubules / Q000648:ultrastructure; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000648:ultrastructure; D016571:Neural Networks, Computer; D011487:Protein Conformation; D012984:Software; D014584:User-Computer Interface
chemical_list: D029721:Drosophila Proteins; D046911:Macromolecular Substances; D020409:Molecular Motor Proteins; C066696:ncd protein, Drosophila; D016547:Kinesins