Ligand excluded surface: A new type of molecular surface

IEEE Transactions on Visualization and Computer Graphics

Volumn 20, Issue 12, 2014, Pages 2486-2495

  Lindow, Norbert ^a   Baum, Daniel ^a   Hege, Hans Christian ^a  

^a ZUSE INSTITUTE BERLIN   (Germany)

Author keywords

cavity analysis; ligand excluded surface; Molecular visualization; solvent excluded surface

Indexed keywords

CAVITY ANALYSIS; MOLECULAR SURFACES; MOLECULAR VISUALIZATION;

EID: 84910049935     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2014.2346404     Document Type: Article

References (48)

1. OpenCL Website, 2014. http://www.khronos.org/opencl/.
2. C. Bajaj and V. Siddavanahalli. Adaptive grid based methods for computing molecular surfaces and properties. Technical report, The University of Texas at Austin, 2006. ICES Report 06-56, Institute for Computational and Engineering Sciences.
3. T. A. Binkowski, S. Naghibzadeh, and J. Liang. CASTp: Computed atlas of surface topography of proteins. Nucleic Acids Research, 31(13):3352-3355, 2003.
4. G. R. Bowman and P. L. Geissler. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites. Proc Natl Acad Sci USA, 109(29):11681-6, Jul 2012.
5. G. P. Brady Jr. and P. F. W. Stouten. Fast prediction and visualization of protein binding pockets with pass. Journal of Computer-Aided Molecular Design, 14(4):383-401, 2000.
6. M. L. Connolly. Molecular surface triangulation. Journal of Applied Crystallography, 18:499-505, 1985.
7. J. Cortés, S. Barbe, M. Erard, and T. Siméon. Encoding molecular motions in voxel maps. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 8:557-563, March 2011.
8. J. Cortés, T. Siméon, V. Ruiz de Angulo, D. Guieysse, M. Remaud-Simon, and V. Tran. A path planning approach for computing large-amplitude motions of flexible molecules. Bioinformatics, 21(suppl 1):i116-i125, 2005.
9. H. Edelsbrunner, M. A. Facello, P. Fu, and J. Liang. Measuring proteins and voids in proteins. In System Sciences, 1995. Proceedings of the Twenty-Eighth Hawaii International Conference on, volume 5, pages 256-264. IEEE, 1995.
10. K. Fischer. Smallest enclosing balls of balls: Combinatorial structure & algorithms. PhD thesis, ETH Zürich, 2005.
11. M. L. Gavrilova and J. Rokne. Updating the topology of the dynamic Voronoi diagram for spheres in Euclidean d-dimensional space. Comput. Aided Geom. Des., 20:231-242, 2003.
12. J. Greer and B. L. Bush. Macromolecular shape and surface maps by solvent exclusion. Proceedings of the National Academy of Sciences, 75(1):303-307, January 1978.
13. M. Hadwiger, C. Sigg, H. Scharsach, K. Bühler, and M. H. Gross. Realtime ray-casting and advanced shading of discrete isosurfaces. Computer Graphics Forum, 24(3):303-312, 2005.
14. M. Haranczyk and J. A. Sethian. Navigating molecular worms inside chemical labyrinths. Proceedings of the National Academy of Sciences, 106(51):21472-21477, 2009.
15. J. C. Hart. Sphere tracing: a geometric method for the antialiased ray tracing of implicit surfaces. The Visual Computer, 12(10):527-545, 1996.
16. M. Hendlich, F. Rippmann, and G. Barnickel. Ligsite: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model, 15(6):359-63, 389, Dec 1997.
17. J. Higo and N. Go. Algorithm for rapid calculation of excluded volume of large molecules. J. Comp. Chem., 10:376-379, 1989.
18. B. Huang. Metapocket: A meta approach to improve protein ligand binding site prediction. OMICS, 13(4):325-330, 2009.
19. B. Huang and M. Schroeder. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol, 6:19, 2006.
20. M. Krone, K. Bidmon, and T. Ertl. Interactive visualization of molecular surface dynamics. IEEE Transactions on Visualization and Computer Graphics, 15(6):1391-1398, 2009.
21. M. Krone, J. E. Stone, T. Ertl, and K. Schulten. Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. Vienna, Austria, 2012. Eurographics Association.
22. M. Krone, M. Falk, S. Rehm, J. Pleiss, and T. Ertl. Interactive exploration of protein cavities. Computer Graphics Forum, 30(3):673-682, 2011.
23. M. Krone, S. Grottel, and T. Ertl. Parallel contour-buildup algorithm for the molecular surface. In Proceedings of IEEE Symposium on Biological Data Visualization (BioVis '11), pages 17-22, 2011.
24. R. A. Laskowski. Surfnet: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of Molecular Graphics, 13:323-330, 1995.
25. A. T. R. Laurie and R. M. Jackson. Q-sitefinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformat-ics, 21(9):1908-1916, 2005.
26. B. Lee and F. M. Richards. The interpretation of protein structures: Esti-mation of static accessibility. Journal of Molecular Biology, 55:379-400, 1971.
27. D. G. Levitt and L. J. Banaszak. Pocket: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph., 10(4):229-234, Dec. 1992.
28. N. Lindow, D. Baum, A.-N. Bondar, and H.-C. Hege. Exploration of cavity dynamics in biomolecular systems. BMC Bioinformatics, 14, 2013.
29. 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.
30. N. Lindow, D. Baum, S. Prohaska, and H.-C. Hege. Accelerated visualization of dynamic molecular surfaces. Comput. Graph. Forum, 29:943-952, 2010.
31. W. E. Lorensen and H. E. Cline. Marching cubes: A high resolution 3d surface construction algorithm. In ACM Siggraph Computer Graphics (Proc. of SIGGRAPH 87), volume 21, pages 163-169. ACM, July 1987.
32. P. Medek, P. Benes, and J. Sochor. Computation of tunnels in protein molecules using Delaunay triangulation. Journal of WSCG, University of West Bohemia, Pilsen, 15(1-3):107-114, 2007.
33. J. Parulek and A. Brambilla. Fast blending scheme for molecular surface representation. IEEE Trans. Vis. Comput. Graph., 19(12):2653-2662, 2013.
34. J. Parulek and I. Viola. Implicit representation of molecular surfaces. In H. Hauser, S. G. Kobourov, and H. Qu, editors, PacificVis, pages 217-224. IEEE, 2012.
35. M. Pavlov and B. Fedorov. Improved technique for calculating X-ray scattering intensity of biopolymers in solution: Evaluation of the form, volume, and surface of a particle. Biopolymers, 22:1507-1522, 1983.
36. Protein Data Bank. http://www.pdb.org.
37. L. H. Pearl and A. Honegger. Generation of molecular surfaces for graphic display. Journal of Molecular Graphics, 1(1):9-12, 1983.
38. M. Petrek, P. Kosinová, J. Koca, and M. Otyepka. MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure, 15(11):1357-1363, Nov 2007.
39. M. Petrek, M. Otyepka, P. Banas, P. Kosinová, J. Koca, and J. Damborsky. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics, 7(1):316+, June 2006.
40. F. M. Richards. Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering, 6:151-176, 1977.
41. M. F. Sanner, A. J. Olson, and J.-C. Spehner. Fast and robust computation of molecular surfaces. In Symposium on Computational Geometry, pages C6-C7, 1995.
42. C. Sigg, T. Weyrich, M. Botsch, and M. Gross. GPU-based ray-casting of quadratic surfaces. In Proceedings of the Eurographics Symposium on Point-Based Graphics, pages 59-65, 2006.
43. O. S. Smart, J. G. Neduvelil, X. Wang, B. A. Wallace, and M. S. Sansom. Hole: a program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph, 14(6):354-60, 376, Dec 1996.
44. R. Sridharamurthy, H. Doraiswamy, S. Patel, R. Varadarajan, and V. Natarajan. Extraction of Robust Voids and Pockets in Proteins. In M. Hlawitschka and T. Weinkauf, editors, EuroVis-Short Papers, pages 67-71, Leipzig, Germany, 2013. Eurographics Association.
45. M. Totrov and R. Abagyan. The contour-buildup algorithm to calculate the analytical molecular surface. Journal of Structural Biology, 116:138-143, 1996.
46. A. Varshney, F. P. B. Jr., J. William, and W. V. Wright. Linearly scalable computation of smooth molecular surfaces. In IEEE Computer Graphics and Applications, volume 14, pages 19-25, 1994.
47. M. Weisel, E. Proschak, and G. Schneider. PocketPicker: analysis of ligand binding-sites with shape descriptors. Chemistry Central Journal, 1(7):1-17, 2007.
48. E. Yaffe, D. Fishelovitch, H. J. Wolfson, D. Halperin, and R. Nussi-nov. MolAxis: Efficient and accurate identification of channels in macro-molecules. Proteins: Structure, Function, and Bioinformatics, 73(1):72-86, 2008.