The Kohonen self-organizing map: A tool for the clustering and alignment of single particles imaged using random conical tilt

Journal of Structural Biology

Volumn 146, Issue 3, 2004, Pages 368-380

  Zampighi, L M ^a   Kavanau, C L ^a   Zampighi, G A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alignment classification; AQP0; Freeze fracture electron microscopy; Random conical tilt; Self organizing maps; Unsupervised networks

Indexed keywords

AQUAPORIN;

ACCURACY; ALGORITHM; ARTICLE; COMPUTER SIMULATION; CYTOPLASM; FREEZE FRACTURE; GEOMETRY; IMAGE ANALYSIS; INTERMETHOD COMPARISON; NOISE; PRIORITY JOURNAL; SIMULATION;

ALGORITHMS; AQUAPORINS; EYE PROTEINS; FREEZE FRACTURING; IMAGING, THREE-DIMENSIONAL; MEMBRANE GLYCOPROTEINS; MEMBRANE PROTEINS; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 1942425201     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2004.01.008     Document Type: Article

References (21)

1. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies. 1996;Academic Press, New York.
2. Fu D., Libson A., Mierke L.J.W., Weitzman C., Nollert P., Krucinsky J., Strroud R.M. Structure of a glycerol-conducting channel and the basis of its selectivity. Science. 290:2000;481-486.
3. Harauz G., Ottensmeyer F.P. Nucleosome reconstruction via phosphorus mapping. Science. 226:1984;936-940.
4. Humphrey W., Dalke A., Schulten K. VMD - visual molecular dynamics. J. Mol. Graph. 14:1996;33-38.
5. Kohonen T. Self-Organization and Associative Memory. 1984;Springer, Berlin. pp. 119-157.
6. Kohonen T. Self-Organizing Maps. third ed. 2001;Springer Series in Information Sciences, Heidelberg.
7. Konig N., Zampighi G.A., Butler P.J. Characterization of the major intrinsic protein (MIP) from bovine lens fibre membranes by electron microscopy and hydrodynamics. J. Mol. Biol. 265:1997;590-602.
8. Lanzavecchia S., Bellon P.L., Radermacher M. Fast and accurate three-dimensional reconstruction from projections with random orientations via Radon transforms. J. Struct. Biol. 128:1999;152-164.
9. Ludtke S.J., Balwin P.R., Chiu W. EMAN: semiautomatic software for high-resolution single-particle reconstruction. J. Struct. Biol. 128:1999;82-97.
10. Marabini R., Carazo J.M. Pattern recognition and classification of images of biological macromolecules using artificial neuronal networks. Biophys. J. 66:1994;1804-1814.
11. Marabini R., Masegosa I.M., San Martín M.C., Marco S., Fernández J.J., de la Fraga L.G., Vaquerizo C., Carazo J.M. Xmipp: An image processing package for electron microscopy. J. Struct. Biol. 116:1996;237-241.
12. Muller T., Gross H., Winkler H., Moor H. High resolution shadowing with pure carbon. Ultramicroscopy. 16:1985;340-348.
13. Pascual-Montano A., Taylor K.A., Winkler H., Pascual-Marqui R.D., Carazo J.M. Quantitative self-organizing maps for clustering electron tomograms. J. Struct. Biol. 138:2002;114-122.
14. Radermacher M. Three-dimensional reconstruction of single particles from random and non-random tilt series. J. Electron Microsc. Tech. 9:1988;359-394.
15. Radermacher M., Wagenknecht T., Verschoor A., Frank J. Three-dimensional reconstruction from a single-exposure random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146:1987;113-136.
16. Sui H., Han B.G., Lee J.K., Wallan P., Jap B.K. Structural basis of water-specific transport through the AQP1 water channel. Nature. 414:2001;872-878.
17. Turk E., Kim O., le Coutre J., Whitelegge J.P., Eskandari S., Lam J.T., Kreman M., Zampighi G.A., Faull K.F., Wright E.M. Molecular characterization of Vibrio parahaemolyticus vSGLT. A model for sodium-coupled sugar cotransporters. J. Biol. Chem. 275:2000;25711-25716.
18. van Heel M., Harauz G., Orlova E.V. A new generation of IMAGIC image processing system. J. Struct. Biol. 116:1996;17-24.
19. Wriggers W., Milligan R.A., McCammon J.A. Situs: a package for docking crystal structures into low resolution maps from electron microscopy. J. Struct. Biol. 125:1999;185-195.
20. Zampighi G.A., Hall J.E., Ehring G.R., Simon S.A. The structural organization and protein composition of lens fiber junctions. J. Cell Biol. 108:1989;2255-2275.
21. Zampighi G.A., Kreman M., Lanzavecchia S., Turk E., Eskandari E., Zampighi L., Wright E.M. Structure of functional AQP0 channels in phospholipid bilayers. J. Mol. Biol. 325:2003;201-210.