Visual analysis of dynamic protein cavities and binding sites

IEEE Pacific Visualization Symposium

Volumn , Issue , 2014, Pages 301-305

  Krone, Michael ^a   Kauker, Daniel ^a   Reina, Guido ^a   Ertl, Thomas ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

Coordinated and Multiple Views; Feature Detection and Tracking; Molecular Visualization; SegmentationEdge and Feature Detection Simulation Output Analysis Life and Medical SciencesBiology and Genetics; Visual Knowledge Discovery

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; VISUALIZATION;

COORDINATED AND MULTIPLE VIEWS; FEATURE DETECTION AND TRACKING; LIFE AND MEDICAL SCIENCES-BIOLOGY AND GENETICS; MOLECULAR VISUALIZATION; VISUAL KNOWLEDGE DISCOVERY;

PROTEINS;

EID: 84899523764     PISSN: 21658765     EISSN: 21658773     Source Type: Conference Proceeding    
DOI: 10.1109/PacificVis.2014.32     Document Type: Conference Paper

References (35)

1. Geomagic, Inc. http://www.geomagic.com/, last accessed 11/15/2013.
2. O. K.-C. Au, C.-L. Tai, H.-K. Chu, D. Cohen-Or, and T.-Y. Lee. Skeleton extraction by mesh contraction. In ACM SIGGRAPH 2008 papers, SIGGRAPH 08, page 44:144:10, New York, NY, USA, 2008. ACM.
3. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The Protein Data Bank. Nucleic Acids Research, 28:235-242, 2000. http://www.pdb.org.
4. J. F. Blinn. A generalization of algebraic surface drawing. ACM Transactions on Graphics, 1:235-256, 1982.
5. J. Cao, A. Tagliasacchi, M. Olson, H. Zhang, and Z. Su. Point cloud skeletons via laplacian based contraction. In Proceedings of the 2010 Shape Modeling International Conference, SMI 10, page 187197, Washington, DC, USA, 2010. IEEE Computer Society.
6. G. Cipriano, G. Phillips, and M. Gleicher. Multi-Scale Surface Descriptors. IEEE Transactions on Visualization and Computer Graphics, 15:1201-1208, 2009.
7. W. L. DeLano. The PyMOL Molecular Graphics System. DeLano Scientific, Palo Alto, CA, USA, 2002. http://www.pymol.org.
8. A. Doi and A. Koide. An Efficient Method of Triangulating Equivalued Surfaces by using Tetrahedral Cells. IEICE Transactions on Communications and Electronics Information Systems, E74:214-224, 1991.
9. G. Grasseau and M. Baaden. MDDriver: Driving Molecular Dynamics codes by coupling with a CPU intensive visualization module, 2007. http://www.baaden. ibpc.fr/projects/mddriver/.
10. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Journal of Chemical Theory and Computation, 4(3):435-447, 2008.
11. W. Humphrey, A. Dalke, and K. Schulten. VMD-Visual Molecular Dynamics. Journal of Molecular Graphics, 14:33-38, 1996.
12. T. Kadonosono, E. Chatani, R. Hayashi, H. Moriyama, and T. Ueki. Minimization of cavity size ensures protein stability and folding: structures of phe46-replaced bovine pancreatic rnase a. Biochemistry, 36(42):10651-8, 2003.
13. J. Kehrer and H. Hauser. Visualization and visual analysis of multifaceted scientific data: A survey. IEEE Transactions on Visualization and Computer Graphics, 19(3):495-513, 2013.
14. D. A. Keim, F. Mansmann, J. Schneidewind, J. Thomas, and H. Ziegler. Visual data mining. chapter Visual Analytics: Scope and Challenges, pages 76-90. Springer-Verlag, 2008.
15. M. Krone, G. Reina, C. Schulz, T. Kulschewski, J. Pleiss, and T. Ertl. Interactive Extraction and Tracking of Biomolecular Surface Features. Computer Graphics Forum, 32(3):331-340, 2013.
16. M. Krone, J. E. Stone, T. Ertl, and K. Schulten. Fast visualization of gaussian density surfaces for molecular dynamics and particle system trajectories. In EuroVis Short Papers, volume 1, pages 67-71, 2012.
17. N. Lindow, D. Baum, A.-N. Bondar, and H.-C. Hege. Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization. In IEEE Symposium on Biological Data Visualization, 2012.
18. N. Lindow, D. Baum, and H.-C. Hege. Voronoi-Based Extraction and Visualization of Molecular Paths. IEEE Transactions on Visualization and Computer Graphics, 17(12):2025-2034, 2011.
19. G. Mistelbauer, A. Morar, A. Varchola, R. Schernthaner, I. Baclija, A. Kochl, A. Kanitsar, S. Bruckner, and M. E. Groller. Vessel Visualization using Curvicircular Feature Aggregation. Computer Graphics Forum, 32(3):231-240, 2013.
20. V. Natarajan, Y. Wang, P. T. Bremer, V. Pascucci, and B. Hamann. Segmenting Molecular Surfaces. Computer Aided Geometric Design, 23(6):495-509, 2006.
21. J. Parulek, C. Turkay, N. Reuter, and I. Viola. Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations. In IEEE Symposium on Biological Data Visualization, 2012.
22. 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.
23. M. Pet?rek, P. Ko?sinova, J. Ko?ca, and M. Otyepka. MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure, 15(11):1357-1363, 2007.
24. M. Pet?rek, M. Otyepka, P. Banas, P. Ko?sinova, J. Koca, and J. Damborsky. CAVER: A new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics, 7(1):316, 2006.
25. M. R. Pivello, I. Larrabide, and R. A. Feijo. An Algorithm for Generating the Centerline of a Branched Tubular Geometry. In Procedings of COBEM, 2007.
26. F. M. Richards. Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering, 6(1):151-176, 1977.
27. J. S. Richardson. The anatomy and taxonomy of protein structure. Advances in protein chemistry, 34:167-339, 09 1981.
28. J. Roche, J. A. Caro, D. R. Norberto, P. Barthe, C. Roumestand, J. L. Schlessman, A. E. Garcia, E. Bertrand Garc?a-Moreno, and C. A. Royer. Cavities Determine the Pressure Unfolding of Proteins. Proceedings of the National Academy of Sciences, 109(18):6945-6950, 2012.
29. P. Schmidtke, A. Bidon-Chanal, F. J. Luque, and X. Barril. MDpocket: Open-Source Cavity Detection and Characterization on Molecular Dynamics Trajectories. Bioinformatics, 27(23):3276-3285, 2011.
30. Schrodinger, LLC. The PyMOL molecular graphics system, version 1.3r1. August 2010.
31. A. Sharf, T. Lewiner, A. Shamir, and L. Kobbelt. On-The-fly curveskeleton computation for 3d shapes. In Eurographics 2007 (Computer Graphics Forum), volume 26, pages 323-328, Prague, october 2007. Eurographics.
32. A. Tagliasacchi, I. Alhashim, M. Olson, and H. Zhang. Mean curvature skeletons. Computer Graphics Forum, 31(5):17351744, 2012.
33. J. Thomas and J. Kielman. Challenges for Visual Analytics. Information Visualization, 8(4):309-314, 2009.
34. M. Weisel, E. Proschak, and G. Schneider. PocketPicker: Analysis of ligand binding-sites with shape descriptors. Chemistry Central Journal, 1(1):7, 2007.
35. J. Yu, Y. Zhou, I. Tanaka, and M. Yao. Roll: A new algorithm for the detection of protein pockets and cavities with a rolling probe sphere. Bioinformatics, pages 46-52, 2010. http://altair. sci.hokudai.ac.jp/g6/service/ pocasa/.