Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking

Journal of Structural Biology

Volumn 143, Issue 3, 2003, Pages 185-200

  Ogura, Toshihiko ^a   Iwasaki, Kenji ^b   Sato, Chikara ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

Cryo electron microscopy; Growing neural gas network; Image classification; Single particle analysis; Topology representing network

Indexed keywords

APOFERRITIN; PROTEIN;

ACCURACY; ARTICLE; CLASSIFICATION; CRYOELECTRON MICROSCOPY; GAS; IMAGING; INTERMETHOD COMPARISON; LEARNING; MASKING; MULTIVARIATE ANALYSIS; NOISE; PRIORITY JOURNAL; PROTEIN STRUCTURE; RELIABILITY; SIMULATION; TECHNIQUE;

EID: 0142059303     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2003.08.005     Document Type: Article

References (32)

1. Carazo J.M., Rivera F.F., Zapata E.L., Radermacher M., Frank J. Fuzzy sets-based classification of electron-microscopy images of biological macromolecules with an application to ribosomal particles. J. Microsc. 157:1990;187-203.
2. Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31:2002;303-319.
3. Frank J., Bretaudiere J.P., Carazo J.M., Verschoor A., Wagenknecht T. Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli. J. Microsc. 150:1988;99-115.
4. Frank J., Goldfarb W., Eisenberg D., Baker T.S. Reconstruction of glutamine synthetase using computer averaging. Ultramicroscopy. 3:1978;283-290.
5. Frank J., Verschoor A., Boublik M. Multivariate statistical analysis of ribosome electron micrographs. L and R lateral views of the 40 S subunit from HeLa cells. J. Mol. Biol. 161:1982;107-133.
6. Fritzke B. Growing cell structures - a self-organizing network for unsupervised and supervised learning. Neural Networks. 7:1994;1441-1460.
7. Fritzke B. A growing neural gas network learns topologies. Tesauro G., Touretzky D.S., Lenn T.K. Advances in Neural Information Processing System. 7:1995;625-632 MIT Press, Cambridge.
8. Fujiyoshi Y. The structural study of membrane proteins by electron crystallography. Adv. Biophys. 35:1998;25-80.
9. Kanaya S., Kinouchi M., Abe T., Kudo Y., Yamada Y., Nishi T., Mori H., Ikemura T. Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene. 276:2001;89-99.
10. Kirkpatrick S., Gelatt C.D., Vecchi M.P. Optimization by simulated annealing. Science. 220:1983;671-680.
11. Kohonen T. Self-organized formation of topologically correct feature maps. Biol. Cybern. 43:1982;59-69.
12. Lambert T.W., Hittle D.C. Optimization of autonomous village electrification systems by simulated annealing. Solar Energy. 68:2000;121-132.
13. Marabini R., Carazo J.M. Pattern recognition and classification of images of biological macromolecules using artificial neural networks. Biophys. J. 66:1994;1804-1814.
14. Marco S., Ortega A., Pardo A., Samitier J. Gas identification with tin oxide sensor array and self-organizing maps: adaptive correction of sensor drifts. IEEE Trans. Instru. Measur. 47:1998;316-321.
15. Martinetz T., Schulten K. Topology representing networks. Neural Networks. 7:1994;507-522.
16. Martinetz T.M., Berkovich S.G., Schulten K.J. Neural-gas network for vector quantization and its application to time-series prediction. IEEE Trans. Neural Networks. 4:1993;558-569.
17. Matadeen R., Patwardhan A., Gowen B., Orlova E.V., Pape T., Cuff M., Mueller F., Brimacombe R., van Heel M. The Escherichia coli large ribosomal subunit at 7.5. Å resolution Structure. 7:1999;1575-1583.
18. Ogura T., Sato C. An automatic particle pickup method using a neural network applicable to low-contrast electron micrographs. J. Struct. Biol. 136:2001;227-238.
19. Ogura, T., Sato, C., 2003. Automatic particle pickup method using a neural network has high accuracy by applying an initial weight derived from eigenimages: a new reference free method for single-particle analysis. J. Struct. Biol. (in press).
20. Pascual-Montano A., Donate L.E., Valle M., Barcena M., Pascual-Marqui R.D., Carazo J.M. A novel neural network technique for analysis and classification of EM single-particle images. J. Struct. Biol. 133:2001;233-245.
21. Radermacher M., Rao V., Grassucci R., Frank J., Timerman A.P., Fleischer S., Wagenknecht T. Cryo-electron microscopy and three-dimensional reconstruction of the calcium release channel/ryanodine receptor from skeletal muscle. J. Cell Biol. 127:1994;411-423.
22. 1-ATPase determined by three-dimensional electron microscopy of single particles. J. Struct. Biol. 135:2001;26-37.
23. Sato C., Sato M., Iwasaki A., Doi T., Engel A. The sodium channel has four domains surrounding a central pore. J. Struct. Biol. 121:1998;314-325.
24. Sato C., Ueno Y., Asai K., Takahashi K., Sato M., Engel A., Fujiyoshi Y. The voltage-sensitive sodium channel is a bell-shaped molecule with several cavities. Nature. 409:2001;1047-1051.
25. Serysheva I.I., Orlova E.V., Chiu W., Sherman M.B., Hamilton S.L., van Heel M. Electron cryomicroscopy and angular reconstitution used to visualize the skeletal muscle calcium release channel. Nat. Struct. Biol. 2:1995;18-24.
26. van Heel M. Multivariate statistical classification of noisy images (randomly oriented biological macromolecules). Ultramicroscopy. 13:1984;165-183.
27. van Heel M., Frank J. Use of multivariate statistics in analysing the images of biological macromolecules. Ultramicroscopy. 6:1981;187-194.
28. van Heel M., Gowen B., Matadeen R., Orlova E.V., Finn R., Pape T., Cohen D., Stark H., Schmidt R., Schatz M., Patwardhan A. Single-particle electron cryo-microscopy: towards atomic resolution. Quart. Rev. Biophys. 33:2000;307-369.
29. van Heel M., Harauz G., Orlova E.V., Schmidt R., Schatz M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116:1996;17-24.
30. Van Hulle M.M. Faithful representations with topographic maps. Neural Networks. 12:1999;803-823.
31. 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.
32. Wriggers W., Milligan R.A., Schulten K., McCammon J.A. Self-organizing neural networks bridge the biomolecular resolution gap. J. Mol. Biol. 284:1998;1247-1254.