ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms

References

• Abeysinghe SS, Baker M, Chiu W, Ju T. 2008. Segmentation-free skeletonization of grayscale volumes for shape understanding. In: IEEE International Conference on Shape Modeling and Applications, 2008. SMI 2008. Stony Brook (NY): IEEE; p. 63–71.
   Google Scholar
• Beck M, Malmström JA, Lange V, Schmidt A, Deutsch EW, Aebersold R. 2009. Visual proteomics of the human pathogen leptospira interrogans. Nat Methods. 6:817–823.
   PubMed Web of Science ®Google Scholar
• Birmanns S, Rusu M, Wriggers W. 2011. Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes. J Struct Biol. 173:428–435.
   PubMed Web of Science ®Google Scholar
• Birmanns S, Wriggers W. 2003. Interactive fitting augmented by force-feedback and virtual reality. J Struct Biol. 144:123–131.
   PubMed Web of Science ®Google Scholar
• Birmanns S, Wriggers W. 2007. Multi-resolution anchor-point registration of biomolecular assemblies and their components. J Struct Biol. 157:271–280.
   PubMed Web of Science ®Google Scholar
• Chacón P, Wriggers W. 2002. Multi-resolution contour-based fitting of macromolecular structures. J Mol Biol. 317:375–384.
   PubMed Web of Science ®Google Scholar
• Cooley JW, Tukey JW. 1965. An algorithm for the machine calculation of complex Fourier series. Math Comput. 19:297–301.
   Web of Science ®Google Scholar
• Engel K, Kraus M, Ertl T. 2001. High-quality pre-integrated volume rendering using hardware-accelerated pixel shading. In: Proceedings of the ACM SIGGRAPH/EUROGRAPHICS Workshop on Graphics Hardware. New York (NY): ACM Press; p. 9–16.
   Google Scholar
• Förster F, Han BG, Beck M. 2010. Visual proteomics. In: Cryo-EM, Part C: Analyses, Interpretation, and Case Studies. Methods in Enzymology. Cambridge (MA): Academic Press; vol. 483, p. 215–243.
   Google Scholar
• Garzón JI, Kovacs J, Abagyan R, Chacón P. 2007. ADP{\_}EM: Fastexhaustive multi-resolution docking for high-throughput coverage. Bioinformatics. 23:427–433.
   PubMed Web of Science ®Google Scholar
• Hoang TV, Cavin X, Ritchie DW. 2013. gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration. J Struct Biol. 184:348–354.
   PubMed Web of Science ®Google Scholar
• Hrabe T, Chen Y, Pfeffer S, Cuellar LK, Mangold AV, Förster F. 2012. PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J Struct Biol. 178:177–188.
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. 1996. VMD -- visual molecular dynamics. J Mol Graphics. 14:33–38.
   PubMed Web of Science ®Google Scholar
• Kniss J, Premoze S, Ikits M, Lefohn A, Hansen C, Praun E. 2003. Gaussian transfer functions for multi-field volume visualization. In: Proceedings IEEE Visualization Conference, Seattle (WA): VIS’03; p. 65.
   Google Scholar
• Kremer JR, Mastronarde DN, McIntosh J. 1996. Computer visualization of three-dimensional image data using imod. J Struct Biol. 116:71–76.
   PubMed Web of Science ®Google Scholar
• Lasker K, Topf M, Sali A, Wolfson HJ. 2009. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol. 388:180–194.
   PubMed Web of Science ®Google Scholar
• Lopéz-Blanco JR, Chacón P. 2013. iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates. J Struct Biol. 184:261–270.
   PubMed Web of Science ®Google Scholar
• Navaza J, Lepault J, Rey F, Alvarez-Rua C, Borge J. 2002. On the fitting of model electron densities into em reconstructions: a reciprocal-space formulation. Acta Crystallogr Sect D: Biol Crystallogr. 58:1820–1825.
   PubMed Web of Science ®Google Scholar
• Nickell S, Förster F, Linaroudis A, Del Net W, Beck F, Hegerl R, Baumeister W, Plitzko JM. 2005. TOM software toolbox: acquisition and analysis for electron tomography. J Struct Biol. 149:227–234.
   PubMed Web of Science ®Google Scholar
• Nickell S, Kofler C, Leis AP, Baumeister W. 2006. A visual approach to proteomics. Nat Rev Mol Cell Biol. 7:225–230.
   PubMed Web of Science ®Google Scholar
• Peng H, Ruan Z, Long F, Simpson JH, Myers EW. 2010. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nat Biotechnol. 28:348–353.
   PubMed Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSF Chimera a visualization system for exploratory research and analysis. J Comput Chem. 25:1605–1612.
   PubMed Web of Science ®Google Scholar
• Pruggnaller S, Mayr M, Frangakis AS. 2008. A visualization and segmentation toolbox for electron microscopy. J Struct Biol. 164:161–165.
   PubMed Web of Science ®Google Scholar
• Rossmann MG. 2000. Fitting atomic models into electron-microscopy maps. Acta Crystallogr Sect D: Biol Crystallogr. 56:1341–1349.
   PubMedGoogle Scholar
• Rullgård H, Öfverstedt LG, Masich S, Daneholt B, Öktem O. 2011. Simulation of transmission electron microscope images of biological specimens. J Microsc. 243:234–256.
   PubMed Web of Science ®Google Scholar
• Stember JN, Wriggers W. 2009. Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion. J Chem Phys. 131:074112. Available from: http://scitation.aip.org/content/aip/journal/jcp/131/7/10.1063/1.3167410
   PubMed Web of Science ®Google Scholar
• Suhre K, Navaza J, Sanejouand YH. 2006. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallogr Sect D: Biol Crystallogr. 62:1098–1100.
   PubMedGoogle Scholar
• Svensson L, Brun A, Nyström I, Sintorn IM. 2011. Registration parameter spaces for molecular electron tomography images. In: Image Analysis and Processing -- ICIAP 2011; Ravenna: LNCS; vol. 6978, p. 403–412.
   Google Scholar
• Svensson L, Nysjö J, Brun A, Nyström I, Sintorn IM. 2012. Rigid template registration in met images using cuda. In: Proceedings International Conference on Computer Vision Theory and Applications, Plzen: VISAPP; p. 418–422.
   Google Scholar
• Svensson L, Sintorn IM. 2013. A probabilistic template model for finding macromolecules in met volume images. In: Pattern Recognition and Image Analysis. Lecture Notes in ComputerScience; vol. 7887. Berlin Heidelberg: Springer; p. 855–862.
   Google Scholar
• Tama F, Miyashita O, Charles LB. 2004. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J Mol Biol. 337:985–999.
   PubMed Web of Science ®Google Scholar
• Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A. 2011. Multifit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res. 39:W167–W170.
   PubMed Web of Science ®Google Scholar
• Trabuco LG, Villa E, Mitra K, Frank J, Schulten K. 2008. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure. 16:673–683.
   PubMed Web of Science ®Google Scholar
• Volkmann N. 2009. Confidence intervals for fitting of atomic models into low-resolution densities. Acta Crystallogr Sect D: Biol Crystallogr. 65:679–689.
   PubMedGoogle Scholar
• Volkmann N, Hanein D. 1999. Quantitative fitting of atomic models into observed densities derived by electron microscopy. J Struct Biol. 125:176–184.
   PubMed Web of Science ®Google Scholar
• Wriggers W. 2010. Using Situs for the integration of multi-resolution structures. Biophys Rev. 2:21–27.
   PubMedGoogle Scholar
• Wriggers W, Agrawal RK, Drew DL, McCammon A, Frank J. 2000. Domain motions of EF-G bound to the 70S ribosome: Insights from a hand-shaking between multi-resolution structures. Biophys J. 79:1670–1678.
   PubMed Web of Science ®Google Scholar
• Wriggers W, Birmanns S. 2001. Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data. J Struct Biol. 133:193–202.
   PubMed Web of Science ®Google Scholar
• Wriggers W, Milligan RA, McCammon JA. 1999. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol. 125:185–195.
   PubMed Web of Science ®Google Scholar
• Xiao C, Rossmann MG. 2007. Interpretation of electron density with stereographic roadmap projections. Journal of Structural Biology. 158:182–187.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Wriggers W. 2006. Local feature analysis: a statistical theory for reproducible essential dynamics of large macromolecules. PROTEINS: Structure, Function, and Bioinformatics. 64:391–403.
   PubMed Web of Science ®Google Scholar