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. and 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. and Steven, A. C. (2008) Computational resources for cryo-electron tomography in Bsoft. J. Struct. Biol. 161(3), 232 – 242.
Radon package
Lanzavecchia S., Bellon P.L. and 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. and 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. and 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. and 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. and 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. and 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. and 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. and 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.
Heymann, J. B., Butan, C., Winkler, D. C., Craven, R. C. and Steven, A. C. (2008) Irregular and semi-regular polyhedral models for Rous sarcoma virus cores. Computational and Mathematical Methods in Medicine, 9(3), 197 - 210.
Nemecek, D., Heymann, J. B., Qiao, J., Mindich, L. and Steven, A. C. (2010) Cryo-electron tomography of bacteriophage φ6 procapsids shows random occupancy of the binding sites for RNA polymerase and packaging NTPase. Journal of Structural Biology, 171(3), 389 - 396.
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. and Heymann, J. B. (1999) Visualizing 3D data obtained from microscopy on the Internet. J. Struct. Biol. 125, 123 - 132.
Sen, A., Heymann, J. B., Cheng, N., Qiao, J., Mindich, L. and Steven, A. C. (2008) Initial location of the RNA-dependent RNA polymerase in the bacteriophage φ6 procapsid determined by cryo-electron microscopy. Journal of Biological Chemistry 283(18), 12227 - 12231.
Trus, B. L., Heymann, J. B., Nealon, K., Cheng, N., Newcomb, W. W., Brown, J. C., Kedes, D. H. and 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
Belnap, D. M., Olson, N. H. and Baker, T. S. (1997) A Method for Establishing the Handedness of Biological Macromolecules. J. Struct. Biol. 120, 44 - 51.
Brinkmann, G. and Dress, A.W.M. (1997) A constructive enumeration of fullerenes. J. Algorithms 23, 345 – 358.
Cardone, G., Grunewald, K. and 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. and Carazo, J. M. (1995) Confidence limits for resolution estimation in image averaging by random subsampling. Ultramicroscopy 60, 385 - 391.
Frangakis, A. S. and Hegerl, R. (2001) Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135(3), 239 - 250.
Frank, J., Verschoor, A. and 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. and 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. and 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. and 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. and Johnson, S. G. (1997) The Fastest Fourier Transform in the West. MIT-LCS-TR-728 (September 1997)
Frigo, M. and 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.
FFTW 2.1.5 is distributed with Bsoft and is compiled as default. FFTW 3.x can be compiled externally and linked during compilation.
Aldus (1992) TIFF revision 6.0. Aldus Corporation, Seattle, Washington.
XML
libxml2 can optionally be linked during compilation.