Bsoft: Image processing and molecular modeling for electron microscopy

Journal of Structural Biology

Volumn 157, Issue 1, 2007, Pages 3-18

  Heymann, J Bernard ^a   Belnap, David M ^a,b  

^a NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES   (United States)

^b Brigham Young University   (United States)

Author keywords

Distributed processing; Image processing workflow; Single particle analysis; Three dimensional image reconstruction; Tomography

Indexed keywords

AMINO ACID; NUCLEIC ACID;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; COMPUTER ANALYSIS; COMPUTER PROGRAM; DENSITY; ELECTRON MICROSCOPY; IMAGE PROCESSING; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PARAMETER; PRIORITY JOURNAL; STANDARD; STRUCTURE ANALYSIS; TECHNIQUE; THREE DIMENSIONAL IMAGING; TOMOGRAPHY; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; SOFTWARE; SOFTWARE DESIGN;

EID: 33845336533     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.06.006     Document Type: Article

References (40)

1. Baker T.S., and Cheng R.H. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J. Struct. Biol. 116 (1996) 120-130
2. Baumeister W., and Steven A.C. Macromolecular electron microscopy in the era of structural genomics. Trends Biochem. Sci. 25 (2000) 624-631
3. Belnap D.M., Grochulski W.D., Olson N.H., and Baker T.S. Use of radial density plots to calibrate image magnification for frozen-hydrated specimens. Ultramicroscopy 48 (1993) 347-358
4. Belnap D.M., Olson N.H., and Baker T.S. A method for establishing the handedness of biological macromolecules. J. Struct. Biol. 120 (1997) 44-51
5. Bowman B.R., Baker M.L., Rixon F.J., Chiu W., and Quiocho F.A. Structure of the herpesvirus major capsid protein. EMBO J. 22 (2003) 757-765
6. Bubeck D., Filman D.J., Cheng N., Steven A.C., Hogle J.M., and Belnap D.M. The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes. J. Virol. 79 (2005) 7745-7755
7. Carazo J.M., Stelzer E.H.K., Engel A., Fita I., Henn C., Machtynger J., McNeil P., Shotton D.M., Chagoyen M., de Alarcón P.A., Fritsch R., Heymann J.B., Kalko S., Pittet J.J., Rodriguez-Tomé P., and Boudier T. Organising multi-dimensional biological image information: the BioImage database. Nucleic Acids Res. 27 (1999) 280-283
8. Cheng N., Trus B.L., Belnap D.M., Newcomb W.W., Brown J.C., and Steven A.C. Handedness of the herpes simplex virus capsid and procapsid. J. Virol. 76 (2002) 7855-7859
9. Crowther R.A., Amos L.A., Finch J.T., De Rosier D.J., and Klug A. Three dimensional reconstructions of spherical viruses by Fourier synthesis from electron micrographs. Nature 226 (1970) 421-425
10. Dai W., Liang Y., and Zhou Z.H. Web portal to an image database for high-resolution three-dimensional reconstruction. J. Struct. Biol. 144 (2003) 238-245
11. Egelman E.H. A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 85 (2000) 225-234
12. Fernandez J.-J., Sanjurjo J., and Carazo J.-M. A spectral estimation approach to contrast transfer function detection in electron microscopy. Ultramicroscopy 68 (1997) 267
13. Frangakis A.S., and Hegerl R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135 (2001) 239-250
14. Frank J., Verschoor A., and Boublik M. Computer averaging of electron micrographs of 40S ribosomal subunits. Science 214 (1981) 1353-1355
15. Fuller S.D., Butcher S.J., Cheng R.H., and Baker T.S. Three-dimensional reconstruction of icosahedral particles-the uncommon line. J. Struct. Biol. 116 (1996) 48-55
16. Grunewald K., Desai P., Winkler D.C., Heymann J.B., Belnap D.M., Baumeister W., and Steven A.C. Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302 (2003) 1396-1398
17. Hall S.R. The STAR file: a new format for electronic data transfer and archiving. J. Chem. Inf. Comput. Sci. 31 (1991) 326-333
18. Harauz G., and van Heel M. Exact filters for general geometry three dimensional reconstruction. Optik 73 (1986) 146-156
19. Heymann J.B. Bsoft: image and molecular processing in electron microscopy. J. Struct. Biol. 133 (2001) 156-169
20. Heymann J.B., and Engel A. Structural clues in the sequences of the aquaporins. J. Mol. Biol. 295 (2000) 1039-1053
21. Heymann J.B., Müller D.J., Landau E.M., Rosenbusch J.P., Pebay-Peyroula E., Büldt G., and Engel A. Charting the surfaces of the purple membrane. J. Struct. Biol. 128 (1999) 243-249
22. Heymann J.B., Pfeiffer M., Hildebrandt V., Kaback R., Fotiadis D., de Groot B., Engel A., Büldt G., Oesterhelt D., and Müller D.J. Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Structure 8 (2000) 643-653
23. Heymann J.B., Cheng N., Newcomb W.W., Trus B.L., Brown J.C., and Steven A.C. Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryo-electron microscopy. Nat. Struct. Biol. 10 (2003) 334-341
24. Heymann J.B., Conway J.F., and Steven A.C. Molecular dynamics of protein complexes from four-dimensional cryo-electron microscopy. J. Struct. Biol. 147 (2004) 291-301
25. Heymann J.B., Chagoyen M., and Belnap D.M. Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. J. Struct. Biol. 151 (2005) 196-207 (Corrigendum, J. Struct. Biol. 153, 312)
26. Heymann J.B., Iwasaki K., Yim Y.I., Cheng N., Belnap D.M., Greene L.E., Eisenberg E., and Steven A.C. Visualization of the binding of Hsc70 ATPase to clathrin baskets: implications for an uncoating mechanism. J. Biol. Chem. 280 (2005) 7156-7161
27. Huiskonen J.T., Kivela H.M., Bamford D.H., and Butcher S.J. The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes. Nat. Struct. Mol. Biol. 11 (2004) 850-856
28. Iancu C.V., Wright E.R., Benjamin J., Tivol W.F., Dias D.P., Murphy G.E., Morrison R.C., Heymann J.B., and Jensen G.J. A "flip-flop" rotation stage for routine dual-axis electron cryotomography. J. Struct. Biol. 151 (2005) 288-297
29. Iancu C.V., Wright E.R., Heymann J.B., and Jensen G.J. A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography. J. Struct. Biol. 153 (2006) 231-240
30. Lanzavecchia S., and Luigi Bellon P. Fast computation of 3D radon transform via a direct Fourier method. Bioinformatics 14 (1998) 212-216
31. Lanzavecchia S., Bellon P.L., and Radermacher M. Fast and accurate three-dimensional reconstruction from projections with random orientations via radon transforms. J. Struct. Biol. 128 (1999) 152-164
32. Leong P.A., Heymann J.B., and Jensen G.J. Peach: a simple Perl-based system for distributed computation and its application to cryo-EM data processing. Structure 13 (2005) 505-511
33. Ludtke S.J., Baldwin P.R., and Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128 (1999) 82-97
34. Ludtke S.J., Nason L., Tu H., Peng L., and Chiu W. Object oriented database and electronic notebook for transmission electron microscopy. Microsc. Microanal. 9 (2003) 556-565
35. Metoz F., Sherman M.B., and Schmid M.F. Adopting a database as a solution to managing electron image data. J. Struct. Biol. 133 (2001) 170-175
36. Mindell J.A., and Grigorieff N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142 (2003) 334-347
37. Murphy G.E., and Jensen G.J. Electron cryotomography of the E. coli pyruvate and 2-oxoglutarate dehydrogenase complexes. Structure 13 (2005) 1765-1773
38. Trus B.L., Heymann J.B., Nealon K., Cheng N., Newcomb W.W., Brown J.C., Kedes D.H., and Steven A.C. Capsid structure of Kaposi's sarcoma-associated herpesvirus, a gammaherpesvirus, compared to an alphaherpesvirus, HSV1, and a betaherpesvirus, CMV. J. Virol. 75 (2001) 2879-2890
39. van Heel M. Do single (ribosome) molecules phase themselves?. Cold Spring Harb. Symp. Quant. Biol. 66 (2001) 77-86
40. Zhu J., Penczek P.A., Schroder R., and Frank J. Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. J. Struct. Biol. 118 (1997) 197-219