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BioBrowser — Visualization of and Access to Macro-Molecular Structures

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Visualization in Medicine and Life Sciences

Part of the book series: Mathematics and Visualization ((MATHVISUAL))

Summary

Based on the results of an interdisciplinary research project the paper addresses the embedding of knowledge about the function of different parts/structures of a macro molecule (protein, DNA, RNA) directly into the 3D model of this molecule. Thereby the 3D visualization becomes an important user interface component when accessing domain-specific knowledge — similar to a web browser enabling its users to access various kinds of information.

In the prototype implementation — named BioBrowser — various information related to bio-research is managed by a database using a fine-grain access control. This also supports restricting the access to parts of the material based on the user privileges. The database is supplied by a SOAP web service so that it is possible (after identifying yourself by a login procedure of course) to query, to change, or to add some information remotely by just using the 3D model of the molecule. All these actions are performed on sub structures of the molecules. These can be selected either by an easy query language or by just picking them in th 3D model with the mouse.

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References

  1. R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M.J. Martin, D.A. Natale, C. O’Donovan, N. Redaschi, and L.S. Yeh. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res., 32:115-119, 2004. http://www.uniprot.org.

    Google Scholar 

  2. B. Boeckmann, A. Bairoch, R. Apweiler, M.-C. Blatter, A. Estreicher, E. Gasteiger, M.J. Martin, K. Michoud, C. O’Donovan, I. Phan, S. Pilbout, and M. Schneider. The SWISS-PROT pro-tein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31:365-370, 2003. http://www.expasy.ch/cgi-bin/sprot-search-ful.

  3. B. Boeckmann, M.-C. Blatter, L. Famiglietti, U. Hinz, L. Lane, B. Roechert, and A. Bairoch. Protein variety and functional diversity: Swiss-Prot annotation in its biological context. Comptes Rendus Biologies, 328:882–899, 2005.

    Article  Google Scholar 

  4. H. J. Bernstein. Recent changes to RasMol, recombining the variants. Trends in Biochemical Sciences, 25:453-455, 2000. www.rasmol.org/.

  5. K. Bryson, L. j. McGuffin, R. L. Marsdenl, J. J. Ward, J. S. Sodhi, and D. T. Jones. Protein structure prediction servers at University College London. Nucleic Acids Research, 33:W36–W38, 2005.

    Article  Google Scholar 

  6. D.L. Bergmann, L. Laaksonen, and A. Laaksonen. Visualization of solvation structures in liquid mixtures. J Mol Graph Model, 15:301–306, 1997.

    Article  Google Scholar 

  7. M. Carson and C.E. Bugg. Algorithm for Ribbon Models of Proteins. J.Mol.Graphics, pages 121-122, 1986.

    Google Scholar 

  8. S. N. Crivelli, E. Eskow, B. Bader, V. Lamberti, R. Byrd, R. Schnabel, and T. Head-Gordon. A physical approach to protein strcuture prediction. Biophysical Journal, 82:36–49, 2002.

    Article  Google Scholar 

  9. M.L. Connolly. Solvent-accessible surfaces of proteins and nucleic acid. Science, 221:709–713, 1983.

    Article  Google Scholar 

  10. Tolga Can, Yujun Wang, Yuan-Fang Wang, and Jianwen Su. FPV: fast protein visualization using Java 3DTM. In Proceedings of the 2003 ACM symposium on Applied computing, pages 88-95. ACM Press, 2003. http://www.ceng.metu.edu.tr/∼tcan/fpv/.

  11. W. L. DeLano. The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA, 2002. http://www.pymol.org.

  12. S. Havemann. Interactive Rendering of Catmull/Clark Surfaces with Crease Edges. The Visual Computer, 18:286–298, 2002.

    Article  Google Scholar 

  13. H. Huang, Z.Z. Hu, B.E. Suzek, and C.H. Wu. The PIR integrated protein databases and data retrieval system. Data Science, 3:163–174, 2004.

    Article  Google Scholar 

  14. Andreas Halm, Lars Offen, and Dieter Fellner. Visualization of Complex Molecular Ribbon Structures at Interactive Rates. In Proceedings of the Information Visualisation, Eighth International Conference on (IV’04), pages 737-744. IEEE Computer Society, 2004.

    Google Scholar 

  15. Andreas Halm, Lars Offen, and Dieter Fellner. BioBrowser: A Frame-work for Fast Protein Visualization. In Ken Brodlie, David Duke, and Ken Joy, editors, Eurographics / IEEE VGTC Symposium on Visualization, pages 287-294, Leeds, United Kingdom, 2005. Eurographics Association.

    Google Scholar 

  16. C. W.V. Hogue. Cn3D: a new generation of three-dimensional molecular structure viewer. Trends in Biochemical Sciences, 22:314-316, 1997. ftp://ftp.ncbi.nih.gov/cn3d/.

  17. Jmol. http://www.jmol.org.

  18. T. Klein and T. Ertl. Illustrating Magnetic Field Lines using a Discrete Particle Model. In Proceedings of the Workshop on Vision, Modelling, and Visualization 2004 (VMV ’04), pages 387-394, 2004.

    Google Scholar 

  19. [KHM+03] Oliver Kreylos, Bernd Hamann, Nelson L. Max, Silvia N. Crivelli, and E. Wes Bethel. Interactive Protein Manipulation. In Proceedings of the 14th IEEE Visualization Conference 2003, 2003.

    Google Scholar 

  20. L. Laaksonen. A graphics program for the analysis and display of molecular dynamics trajectories. J Mol Graph, 10:33–34, 1992.

    Article  Google Scholar 

  21. B. Lee and F. M. Richards. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol., 55:379–400, 1971.

    Article  Google Scholar 

  22. S. M. Larson, C. D. Snow, M. R. Shirts, and V. S. Pande. Computational Genomics: Theory and Application, chapter Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computationla biology. Horizon Press, 2004.

    Google Scholar 

  23. L. J. McGuffin, K. Bryson, and D. T. Jones. The PSIPRED protein structure prediction server. Bioinformatics Applications Note, 16:404–405,2000.

    Google Scholar 

  24. [PGH+04] E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin. UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Compu-tational Chemistry, 25:1605-1612, 2004. http://www.cgl.ucsf.edu/chimera/.

    Google Scholar 

  25. J. S. Richardson. The anatomy and taxonomy of protein structure. Adv. Protein Chem., pages 167-339, 1981.

    Google Scholar 

  26. J. L. Sussman, D. Lin, J. Jiang, N. O. Manning, J. Prilusky, O. Ritter, and E.E. Abola. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr., D 54:1078-1084, 1998. http://www.pdb.org.

    Google Scholar 

  27. H. Steen and M. Mann. The abc’s (and xyz’s) of peptide sequencing. Nature Reviews Molecular Cell Biology, 5:699–711, 2004.

    Article  Google Scholar 

  28. R. Sayle and E. J. Milner-White. RasMol: Biomolecular graphics for all. Trends Biochem. Sci., 20:374, 1995. http://www.rasmol.org/.

  29. Michel F. Sanner and Arthur J. Olson. Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers, 38:305–320, 1996.

    Article  Google Scholar 

  30. W3C. SOAP Version 1.2 Part 0: Primer.

    Google Scholar 

  31. Y. Zhang and J. Skolnick. The protein structure prediction problem could be solved using the current pdb library. Proc. Natl. Acad. Sci., 102:1029–1034, 2005.

    Article  Google Scholar 

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Offen, L., Fellner, D. (2008). BioBrowser — Visualization of and Access to Macro-Molecular Structures. In: Linsen, L., Hagen, H., Hamann, B. (eds) Visualization in Medicine and Life Sciences. Mathematics and Visualization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72630-2_15

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