Primary Bsoft papers
Heymann, J. B. (2001) Bsoft: Image and molecular processing in electron microscopy. J. Struct. Biol. 133(2/3), 156 - 169.
Heymann, J. B. & Belnap, D. M. (2007) Bsoft: Image processing and molecular modeling for electron microscopy. J. Struct. Biol. 157(1), 3 - 18.
Heymann, J. B., Cardone, G., Winkler, D. C. & Steven, A. C. (2007) Computational resources for cryo-electron tomography in Bsoft. J. Struct. Biol. 161(3), 232 - 242.
Radon package
Lanzavecchia S., Bellon P.L. & Radermacher M. (1999) Fast and accurate three dimensional reconstruction from projections with random orientations via Radon transforms. J. Struct. Biol. 128, 152 - 164.
Lanzavecchia S., Cantele F., Radermacher M. & Bellon P.L. (2002) Symmetry embedding in the reconstruction of macromolecular assemblies via the discrete Radon transform. J. Struct. Biol., 137, 259 - 272.
Peach distributed processing system
Leong, P.A., Heymann, J.B. & Jensen, G.J. (2005) Peach: A simple perl-based system for distributed computation and its application to Cryo-EM data processing. Structure 13(4), 505 - 511.
Use of Bsoft
Grünewald, K., Desai, P., Winkler, D. C., Heymann, J. B., Belnap, D. M., Baumeister, W. and Steven, A. C. (2003). Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302(5649): 1396 - 1398.
Harris, A., Cardone, G., Winkler, D. C. , Heymann, J. B., Brecher, M., White, J. M., Steven, A. C. (2006) Influenza virus pleiomorphy characterized by cryoelectron tomography. Proceedings of the National Academy of Sciences of the U. S. A. 103(50): 19123 - 19127.
Heymann, J. B. & Engel, A. (2000) Structural clues in the sequences of the aquaporins. J. Mol. Biol. 295, 1039 - 1053.
Heymann, J. B., Müller, D. J., Landau, E. M., Rosenbusch, J. P., Pebay-Peyroula, E., Büldt, G. & Engel, A. (1999) Charting the surfaces of the purple membrane. J. Struct. Biol. 128(3), 243 - 249.
Heymann, J. B., Pfeiffer, M., Hildebrandt, V., Kaback, R., Fotiadis, D., de Groot, B., Engel, A., Büldt, G., Oesterhelt, D. & Müller, D. J. (2000). Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Structure 8, 643 - 653.
Heymann, J.B., Cheng, N., Newcomb, W.W., Trus, B.L., Brown, J.C. & Steven, A.C. (2003) Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryo-electron microscopy. Nature Structural Biology 10(5), 334 - 341.
Heymann, J.B., Iwasaki, K., Yim, Y.-I., Cheng, N., Belnap, D.M., Greene, L.E., Eisenberg, E. & Stevens, A.C. (2005) Visualization of the binding of Hsc70 ATPase to clathrin baskets: Implications for an uncoating mechanism. Journal of Biological Chemistry 280(8), 7156 - 7161.
Iancu, C. V., Wright, E. R., Benjamin, J., Tivol, W. F., Dias, D. P., Murphy, G. E., Heymann, J. B., and Jensen, G. J. (2005) A "flip-flop" rotation stage for routine dual-axis electron cryotomography. Journal of Structural Biology 151(3): 288 - 297.
Iancu, C. V., Wright, E. R., Heymann, J. B., and Jensen, G. J. (2006) A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography. Journal of Structural Biology 153(3): 231 - 240.
Ortega, J., Heymann, J. B., Kajava, A. V., Rechsteiner, M. and Steven, A. C. (2005) The Axial Channel of the 20S Proteasome Opens Upon Binding of the PA200 Activator. Journal of Molecular Biology 346: 1221 - 1227.
Pittet, J.-J., Henn, C., Engel, A. & Heymann, J. B. (1999) Visualizing 3D data obtained from microscopy on the Internet. J. Struct. Biol. 125, 123 - 132.
Trus, B. L., Heymann, J. B., Nealon, K., Cheng, N., Newcomb, W. W., Brown, J. C., Kedes, D. H. & Steven, A. C. (2001) Capsid structure of Kaposi's sarcoma-associated herpesvirus, a gammaherpesvirus, compared to an alphaherpesvirus, herpes simplex virus type 1, and a betaherpesvirus, cytomegalovirus. J. Virol., 75(6), 2879 - 2890.
Algorithms used in Bsoft
Cardone, G., Grunewald, K. &Steven AC. (2005) A resolution criterion for electron tomography based on cross-validation. J Struct Biol. 151(2), 117-129.
Cowley, J. M. (1995) Diffraction Physics. 3rd Rev. Ed. Elsevier Science, Amsterdam. (Multislice image simulation)
de la Fraga, L. G., Dopazo, J. & Carazo, J. M. (1995) Confidence limits for resolution estimation in image averaging by random subsampling. Ultramicroscopy 60, 385 - 391.
Frangakis, A. S. & Hegerl, R. (2001) Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J Struct Biol. 135(3), 239 - 250.
Frank, J., Verschoor, A. & Miloslav Boublik, M. (1981) Computer Averaging of Electron Micrographs of 40S Ribosomal Subunits. Science 214, 1353 - 1355.
Frey, B. J. and D. Dueck (2007) Clustering by passing messages between data points. Science 315, 972 - 976.
Gobel, U., Sander, C., Schneider, R. & Valencia, A. (1994) Correlated mutations and residue contacts in proteins. Proteins 18, 309 - 317.
Hall, S. R. (1991) The STAR file: A new format for electronic data transfer and archiving. J. Chem. Inform. Comput. Sci. 31, 326 - 333.
Hall, S. R., Allen, F. H. and Brown, I. D. (1991) The Crystallographic Information File (CIF): a new standard archive file for crystallography[1]. Acta Crystall. A47, 655 - 685.
Press, W.H., Teukolsky, S.A., Vetterling, W.T. & Flannery, B.P. (1992) Numerical Recipes in C. 2nd ed. Cambridge University Press, Cambridge. (Downhill simplex method of Nelder and Mead, Student's t-test, poisson distributed random numbers, LU decomposition, singular value decomposition, eigen analysis, factorial)
Saxton, W. O. and Baumeister, W. (1982) The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 127, 127 - 138.
Unser, M., Trus, B. L. and Steven, A. C. (1987) A new resolution criterion based on spectral signal-to-noise ratios. Ultramicr. 23, 39 - 52.
Winkelmann, D. A., Baker, T. S. & Rayment, I. (1991) Three-dimensional structure of myosin subfragment-1 from electron microscopy of sectioned crystals. J. Cell Biology 114, 701 - 713.
Software coopted in Bsoft
Frigo, M. & Johnson, S. G. (1997) The Fastest Fourier Transform in the West. MIT-LCS-TR-728 (September 1997)
Frigo, M. & Johnson, S. G. (1998) FFTW: An adaptive software architecture for the FFT. In Proceedings of the ICASSP eds.), p. 1381.
Frigo, M. (1999) A fast fourier transform compiler. In Proceedings of the Conference on Programming Language Design and Implementation eds.), ACM SIGPLAN, Atlanta, Georgia.
Aldus (1992) TIFF revision 6.0. Aldus Corporation, Seattle, Washington.
