Parallel Contour-Buildup algorithm for the molecular surface

IEEE Symposium on Biological Data Visualization 2011, BioVis 2011 - Proceedings

Volumn , Issue , 2011, Pages 17-22

  Krone, Michael ^a   Grottel, Sebastian ^a   Ertl, Thomas ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

I.3.1 Computer Graphics : Hardware Architecture Parallel processing; I.3.5 Computer Graphics : Computational Geometry and Object Modeling Surface representations; I.3.7 Computer Graphics : Three Dimensional Graphics and Realism Raytracing; J.3 Computer Applications : Life and Medical Sciences Biology and genetics

Indexed keywords

CONSUMER GRAPHICS CARDS; DATA SETS; GRAPHICS HARDWARE; I.3.1 [COMPUTER GRAPHICS]: HARDWARE ARCHITECTURE - PARALLEL PROCESSING; I.3.7 [COMPUTER GRAPHICS]: THREE-DIMENSIONAL GRAPHICS AND REALISM; INTERACTIVE VISUALIZATIONS; J.3 [COMPUTER APPLICATIONS]: LIFE AND MEDICAL SCIENCES BIOLOGY AND GENETICS; MEDICAL RESEARCH; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SURFACES; MOLECULE SURFACE; ORIGINAL ALGORITHMS; PARALLEL PROCESSING; PROGRAMMING LANGUAGE; SPATIAL RELATIONS; SURFACE REPRESENTATION; SURFACE VISUALIZATION; TIME-DEPENDENT DATA; VISUAL REPRESENTATIONS;

ALGORITHMS; COMPUTATIONAL GEOMETRY; COMPUTER ARCHITECTURE; COMPUTER HARDWARE; COMPUTER SIMULATION; INTERACTIVE COMPUTER GRAPHICS; MOLECULAR DYNAMICS; MOLECULES; OPTIMIZATION; THREE DIMENSIONAL COMPUTER GRAPHICS; VIDEO SIGNAL PROCESSING; VISUALIZATION;

DATA VISUALIZATION;

EID: 84255162914     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BioVis.2011.6094043     Document Type: Conference Paper

References (35)

1. CUDA Data Parallel Primitives Library, April 2011. http://gpgpu.org/ developer/cudpp.
2. C. L. Bajaj, P. Djeu, V. Siddavanahalli, and A. Thane. TexMol: Interactive visual exploration of large flexible multi-component molecular complexes. In IEEE Visualization, pages 243-250, Oct 2004.
3. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The Protein Data Bank. Nucl. Acids Res., 28:235-242, 2000. http://www.pdb.org/.
4. M. L. Connolly. Analytical molecular surface calculation. J. Appl. Cryst., 16:548-558, 1983.
5. M. L. Connolly. Molecular surface Triangulation. Journal of Applied Crystallography, 18(6):499-505, Dec 1985.
6. R. de Toledo, B. Lévy, and J.-C. Paul. Iterative methods for visualization of implicit surfaces on GPU. In ISVC, International Symposium on Visual Computing, pages 598-609, Nov 2007.
7. W. L. DeLano. The PyMOL Molecular Graphics System. DeLano Scientific, Palo Alto, CA, USA, 2002. http://www.pymol.org.
8. H. Edelsbrunner and E. P. Mücke. Three-dimensional alpha shapes. ACM Trans. Graph., 13(1):43-72, 1994.
9. S. Green. Cuda particles. Technical report, NVIDIA Corporation, 2008.
10. J. Greer and B. L. Bush. Macromolecular shape and surface maps by solvent exclusion. In Proceedings of the National Academy of Science, pages 303-307, Jan 1978.
11. S. Grottel, G. Reina, and T. Ertl. Optimized Data Transfer for Timedependent, GPU-based Glyphs. In Proceedings of IEEE Pacific Visualization Symposium 2009, pages 65-72, 2009. http://www.vis.unistuttgart.de/eng/research/ fields/perf/.
12. S. Gumhold. Splatting illuminated ellipsoids with depth correction. In Proceedings of VMV, pages 245 - 252, 2003.
13. A. Halm, L. Offen, and D. W. Fellner. BioBrowser: A framework for fast protein visualization. In EuroVis05: IEEE VGTC Symposium on Visualization, pages 287-294, 2005.
14. D. Herbison-Evans. Solving quartics and cubics for graphics. In A.W. Paeth, editor, Graphics Gems V, pages 3-15. 1. edition, 1995.
15. W. Humphrey, A. Dalke, and K. Schulten. VMD - Visual Molecular Dynamics. Journal of Molecular Graphics, 14:33-38, 1996.
16. T. Klein and T. Ertl. Illustrating magnetic field lines using a discrete particle model. In Proceedings of VMV, pages 387-394, 2004.
17. M. Krone, K. Bidmon, and T. Ertl. Interactive visualization of molecular surface dynamics. IEEE Transactions on Visualization and Computer Graphics, 15(6), 2009.
18. N. Lindow, D. Baum, S. Prohaska, and H.-C. Hege. Accelerated visualization of dynamic molecular surfaces. Computer Graphics Forum, 29:943-952, 2010.
19. C. Loop and J. Blinn. Real-time GPU rendering of piecewise algebraic surfaces. ACM Trans. Graph., 25(3):664-670, 2006.
20. G. Perrot, B. Cheng, K. D. Gibson, J. Vila, K. A. Palmer, A. Nayeem, B. Maigret, and H. A. Scheraga. MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives. J. Comput. Chem., 13(1):1-11, 1992.
21. 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. J. Comput. Chem., 25(13):1605-1612, Oct 2004.
22. G. Reina and T. Ertl. Hardware-accelerated glyphs for mono- and dipoles in molecular dynamics visualization. In EuroVis05: IEEE VGTC Symposium on Visualization, pages 177-182, 2005.
23. F. M. Richards. Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering, 6(1):151-176, 1977.
24. J. S. Richardson. The anatomy and taxonomy of protein structure. Advances in protein chemistry, 34:167-339, 09 1981.
25. J. Ryu, Y. Cho, and D.-S. Kim. Triangulation of molecular surfaces. Comput. Aided Des., 41:463-478, June 2009.
26. J. Ryu, R. Park, and D.-S. Kim. Molecular surfaces on proteins via beta shapes. Computer-Aided Design, 39(12):1042-1057, 2007.
27. M. F. Sanner and A. J. Olson. Real time surface reconstruction for moving molecular fragments. In Pacific Symposium on Biocomputing '97, pages 385-396, 1997.
28. M. F. Sanner, A. J. Olson, and J.-C. Spehner. Reduced surface: An efficient way to compute molecular surfaces. Biopolymers, 38(3):305-320, Dec 1996.
29. J. M. Singh and P. Narayanan. Real-Time Ray Tracing of Implicit Surfaces on the GPU. IEEE Transactions on Visualization and Computer Graphics, 99:261-272, 2009.
30. J. M. Singh and P. J. Narayanan. Real-time ray-tracing of implicit surfaces on the gpu. Technical report iiit/tr/2007/72, International Institute of Information Technology, Hyderabad, India, Jul 2007.
31. M. Tarini, P. Cignoni, and C. Montani. Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics, 12(5):1237-1244, 2006.
32. R. Toledo and B. Levy. Visualization of industrial structures with implicit gpu primitives. In Proceedings of the 4th International Symposium on Advances in Visual Computing, ISVC '08, pages 139-150, Berlin, Heidelberg, 2008. Springer-Verlag.
33. M. Totrov and R. Abagyan. The contour-buildup algorithm to calculate the analytical molecular surface. Journal of Structural Biology, 116:138-143, 1995.
34. A. Varshney, F. P. Brooks, and W. V. Wright. Linearly scalable computation of smooth molecular surfaces. IEEE Computer Graphics and Applications, 14(5):19-25, 1994.
35. W. Zhao, G. Xu, and C. Bajaj. An algebraic spline model of molecular surfaces. In SPM '07: Proceedings of the 2007 ACM symposium on Solid and physical modeling, pages 297-302, 2007.