Two-level approach to efficient visualization of protein dynamics

IEEE Transactions on Visualization and Computer Graphics

Volumn 13, Issue 6, 2007, Pages 1616-1623

  Lampe, Ove Daae ^b   Viola, Ivan ^a,c   Reuter, Nathalie ^c   Hauser, Helwig ^a,c  

^a IEEE   (Norway)

^b CHRISTIAN MICHELSEN RESEARCH AS   (Norway)

^c UNIVERSITY OF BERGEN   (Norway)

Author keywords

Hardware acceleration; Molecular visualization; Protein dynamics

Indexed keywords

HARDWARE ACCELERATION; HIERARCHICAL MODEL; MOLECULAR VISUALIZATION; PROTEIN DYNAMICS;

BIOINFORMATICS; COMPUTER SUPPORTED COOPERATIVE WORK; GEOMETRY; VOLUME RENDERING;

VISUALIZATION;

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER ASSISTED DIAGNOSIS; COMPUTER GRAPHICS; COMPUTER SIMULATION; IMAGE ENHANCEMENT; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN FOLDING; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

ALGORITHMS; COMPUTER GRAPHICS; COMPUTER SIMULATION; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SURFACE PROPERTIES;

EID: 35948969799     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2007.70517     Document Type: Article

References (33)

1. ATI web page on hardware specs, http://www.ati.com/, 2007.
2. C. L. Brooks, M. Karplus, and M. Pettitt. Proteins, a theoretical perspective of dynamics, structure and thermodynamics. John Wiley and Sons, 1988.
3. M. S. T. Carpendale, D. J. Cowperthwaite, and F. D. Fracchia. Distortion viewing techniques for 3-dimensional data. In Proceedings of IEEE Symposium on Information Visualization, pages 46-53, 1996.
4. P. Cignoni, C. Montani, and R. Scopigno. Magicsphere: an insight tool for 3d data visualization. In Computer Graphics Forum, 13, pages 317-328, 1994.
5. S. Gumhold. Splatting illuminated ellipsoids with depth correction. In Proceedings of Vision, Modelling and Visualization Workshop, pages 245-252, 2003.
6. X. Hao, A. Varshney, and S. Sukharev. Real-time visualization of large time-varying molecules. In Proceedings of High-Performance Computing Symposium, 2004.
7. H. Hauser. Scientific Visualization: The Visual Extraction of Knowledge from Data, chapter Generalizing Focus+Context Visualization, pages 305-327. Springer-Verlag, 2005.
8. S. Hayward. Normal mode analysis of biological molecules. In Computational biochemistry and biophysics, pages 153-168, 2001.
9. K. Hinsen. The molecular modeling toolkit: a new approach to molecular simulations. Journal of Computational Chemistry, 21:79-85, 2000.
10. S. Hollup, G. Sælensminde, and N. Reuter. WEBnma: a web application for normal mode analyses of proteins. BMC Bioinformatics, 6(1):52, 2005.
11. H. Huitema and R. van Liere. Interactive visualization of protein dynamics. In Proceedings of IEEE Visualization, pages 465-468, 2000.
12. W. F. Humphrey, A. Dalke, and K. Schulten. VMD - visual molecular dynamics. Journal of Molecular Graphics and Modelling, 14:33-38, 1996.
13. S. Jeschke, M. Wimmer, and W. Purgathofer. Image-based representations for accelerated rendering of complex scenes. State of The Art Report Eurographics, 2005.
14. L.H.Weaver, M.G.Gruetter, and B.W.Matthews. he refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue. JMol Biol, 245:54-68, 1995.
15. J.-J. L. N. Reuter, K. Hinsen. Transconformations of the sercal ca-atpase: A normal mode study. Biophysical Journal, 85:2186-2197, 2003.
16. D. L. Nelson, and M. M. Cox. Lehninger. Principles of Biochemistry, 3rd edition. Macmillan Press Worth Publishers, 2000.
17. S. Noskov and B. Roux. Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. Journal of General Physiology, 129(2):135-143, 2007.
18. NVIDIA web page on hardware specs, http://www.nvidia.com/, 2007.
19. Opengl web site, http://www.opengl.org/, 2007.
20. An information portal to biological, macromolecular structures. http://www.pdb.org/, 2007.
21. J. F. Prins, J. Hermans, G. Mann, L. S. Nyland, and M. Simons. A virtual environment for steered molecular dynamics. Future Generation Computer Systems, 15(4):485-495, 1999.
22. R.Huber and J.Deisenhofer. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. acta crystallogr, 39:480, 1983.
23. M. Schirski, T. Kuhlen, M. Hopp, P. Adomeit, S. Pischinger, and C. Bischof. Efficient visualization of large amounts of particle trajectories in virtual environments using virtual tubelets. In Proceedings of the ACM SIGGRAPH international conference on Virtual. Reality continuum and its applications in industry, pages 141-147, 2004.
24. SGI techpubs library, http://techpubs.sgi.comy. http://techpubs.sgi.com/, 2007.
25. C. Stall, S. Gumhold, and H.-P. Seidel. Visualization with stylized line primitives. In Proceedings of IEEE Visualization, pages 695-702, 2005.
26. J. E. Stone, J. Gullingsrud, and K. Schulten. A system for interactive molecular dynamics simulation. In Proceedings of the 2001 symposium on Interactive 3D graphics, pages 191-194, 2001.
27. M. Tarini, P. Cignoni, and C. Montani. Ambient occlusion and edge cueing to enhance real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2006), 12(5):1237-1244, 2006.
28. D. P. Tieleman. Computer simulations of transport through membranes: Passive diffusion, pores, channels and transporters. Clinical and Experimental Pharmacology and Physiology, 33(10):893-903, 2006.
29. J. Viega, M. J. Conway, G. Williams, and R. Pausch. 3d magic lenses. In Proceedings of ACM Symposium on User Interface Software and Technology, pages 51-58, 1996.
30. C. Ware and G. Franck. Evaluating stereo and motion cues for visualizing information nets in three dimensions. ACM Transactions on Graphics, 15(2):121-140, 1996.
31. S. D. Young, B. D. Adelstein, and S. R. Ellis. Demand characteristics in assessing motion sickness in a virtual environment: Or does taking a motion sickness questionnaire make you sick? IEEE Transactions on Visualization and Computer Graphics, 13(3):422-428, 2007.
32. Y.Y.Guo, F.Blocker, F.Xiao, and P.Guo. Construction and 3-d computer modeling of connector arrays with tetragonal to decagonal transition induced by prna of phi29 dna-packaging motor. J Nanosci Nanotechnol, 5:856-863, 2005.
33. Z.Xu, A.L.Horwich, and P.B.Sigler. The crystal structure of the asymmetric groel-groes-(adp)7 chaperonin complex. Nature, 388:741-750, 1997.