Interactive GPU-based generation of solvent-excluded surfaces

Abstract

The solvent-excluded surface (SES) is a popular molecular representation that gives the boundary of the molecular volume with respect to a specific solvent. SESs depict which areas of a molecule are accessible by a specific solvent, which is represented as a spherical probe. Despite the popularity of SESs, their generation is still a compute-intensive process, which is often performed in a preprocessing stage prior to the actual rendering (except for small models). For dynamic data or varying probe radii, however, such a preprocessing is not feasible as it prevents interactive visual analysis. Thus, we present a novel approach for the on-the-fly generation of SESs, a highly parallelizable, grid-based algorithm where the SES is rendered using ray-marching. By exploiting modern GPUs, we are able to rapidly generate SESs directly within the mapping stage of the visualization pipeline. Our algorithm can be applied to large time-varying molecules and is scalable, as it can progressively refine the SES if GPU capabilities are insufficient. In this paper, we show how our algorithm is realized and how smooth transitions are achieved during progressive refinement. We further show visual results obtained from real-world data and discuss the performance obtained, which improves upon previous techniques in both the size of the molecules that can be handled and the resulting frame rate.

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References

  1. 1.

    Behley, J., Steinhage, V., Cremers, A.B.: Efficient radius neighbor search in three-dimensional point clouds. In: 2015 IEEE International Conference on Robotics and Automation (ICRA), pp. 3625–3630 (2015)

  2. 2.

    Blinn, J.F.: A generalization of algebraic surface drawing. ACM Trans. Graph. 1(3), 235–256 (1982)

    Article  Google Scholar 

  3. 3.

    Can, T., Chen, C.I., Wang, Y.F.: Efficient molecular surface generation using level-set methods. J. Mol. Graph. Model. 25(4), 442–454 (2006)

    Article  Google Scholar 

  4. 4.

    Connolly, M.L.: Analytical molecular surface calculation. J. Appl. Crystallogr. 16(5), 548–558 (1983)

    Article  Google Scholar 

  5. 5.

    Edelsbrunner, H., Mücke, E.P.: Three-dimensional alpha shapes. ACM Trans. Graph. 13(1), 43–72 (1994)

    Article  MATH  Google Scholar 

  6. 6.

    Green, S.: White paper: CUDA particles. Technical reports (2007)

  7. 7.

    Greer, J., Bush, B.L.: Macromolecular shape and surface maps by solvent exclusion. Proc. Natl. Acad. Sci. 75, 303–307 (1978)

    Article  Google Scholar 

  8. 8.

    Grottel, S., Krone, M., Müller, C., Reina, G., Ertl, T.: MegaMol—a prototyping framework for particle-based visualization. IEEE Trans. Vis. Comput. Graph. 21(2), 201–214 (2015)

    Article  Google Scholar 

  9. 9.

    Hadwiger, M., Sigg, C., Scharsach, H., Bhler, K., Gross, M.: Real-time ray-casting and advanced shading of discrete isosurfaces. Comput. Graph. Forum 24(3), 303–312 (2005)

    Article  Google Scholar 

  10. 10.

    Hermosilla, P., Guallar, V., Vinacua, A., Vázquez, P.: High quality illustrative effects for molecular rendering. Comput. Graph. 24, 113–120 (2015)

    Google Scholar 

  11. 11.

    Hoetzlein, R.C.: Fast fixed-radius nearest neighbors: interactive million-particle fluids. In: GPU Technology Conference (2014)

  12. 12.

    Jurcik, A., Parulek, J., Sochor, J., Kozlikova, B.: Accelerated visualization of transparent molecular surfaces in molecular dynamics. In: IEEE Pacific Visualization Symposium, pp. 112–119 (2016)

  13. 13.

    Kozlíková, B., Krone, M., Lindow, N., Falk, M., Baaden, M., Baum, D., Viola, I., Parulek, J., Hege, H.C.: Visualization of molecular structure: state of the art revisited. Comput. Graph. Forum (2016)

  14. 14.

    Krone, M., Bidmon, K., Ertl, T.: Interactive visualization of molecular surface dynamics. IEEE Trans. Vis. Comput. Graph. 15(6), 1391–1398 (2009)

    Article  Google Scholar 

  15. 15.

    Krone, M., Grottel, S., Ertl, T.: Parallel contour-buildup algorithm for the molecular surface. In: IEEE Symposium on Biological Data Visualization, pp. 17–22 (2011)

  16. 16.

    Krone, M., Stone, J.E., Ertl, T., Schulten, K.: Fast visualization of gaussian density surfaces for molecular dynamics and particle system trajectories. EuroVis-Short Pap. 1, 67–71 (2012)

    Google Scholar 

  17. 17.

    Lindow, N., Baum, D., Hege, H.C.: Ligand excluded surface: a new type of molecular surface. IEEE Trans. Vis. Comput. Graph. 20(12), 2486–2495 (2014)

    Article  Google Scholar 

  18. 18.

    Lindow, N., Baum, D., Prohaska, S., Hege, H.C.: Accelerated visualization of dynamic molecular surfaces. Comput. Graph. Forum 29(3), 943–952 (2010)

    Article  Google Scholar 

  19. 19.

    Lorensen, W.E., Cline, H.E.: Marching cubes: a high resolution 3D surface construction algorithm. ACM SIGGRAPH Comput. Graph. Interact. Tech. 21, 163–169 (1987)

    Article  Google Scholar 

  20. 20.

    Parulek, J., Viola, I.: Implicit representation of molecular surfaces. In: 2012 IEEE Pacific Visualization Symposium, pp. 217–224 (2012). doi:10.1109/PacificVis.2012.6183594

  21. 21.

    Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.: UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25(13), 1605–1612 (2004)

    Article  Google Scholar 

  22. 22.

    Richards, F.M.: Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng. 6(1), 151–176 (1977)

    Article  Google Scholar 

  23. 23.

    Sanner, M.F., Olson, A.J., Spehner, J.C.: Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38(3), 305–320 (1996)

    Article  Google Scholar 

  24. 24.

    Skånberg, R., Vázquez, P.P., Guallar, V., Ropinski, T.: Real-time molecular visualization supporting diffuse interreflections and ambient occlusion. IEEE Trans. Vis. Comput. Graph. 22(1), 718–727 (2016)

    Article  Google Scholar 

  25. 25.

    Tarini, M., Cignoni, P., Montani, C.: Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans. Vis. Comput. Graph. 12(5), 1237–1244 (2006)

    Article  Google Scholar 

  26. 26.

    Totrov, M., Abagyan, R.: The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 116, 138–143 (1995)

    Article  Google Scholar 

  27. 27.

    Varshney, A., Brooks, F.P., Wright, W.V.: Linearly scalable computation of smooth molecular surfaces. IEEE Comput. Graph. Appl. 14(5), 19–25 (1994)

    Article  Google Scholar 

  28. 28.

    Xu, D., Zhang, Y.: Generating triangulated macromolecular surfaces by Euclidean distance transform. PLoS ONE 4(12), e8140 (2009)

    Article  Google Scholar 

  29. 29.

    Yu, Z.: A List-based method for fast generation of molecular surfaces. In: International Conference of the IEEE Engineering in Medicine and Biology Society, vol. 31, pp. 5909–5912 (2009)

Download references

Acknowledgements

This work has been partially supported by Grant TIN2014-52211-C2-1-R and Grant CTQ2016-79138-R from the Spanish Ministerio de Economía y Competitividad with FEDER funds, and by the German Research Foundation (DFG) as part of Collaborative Research Center SFB 716.

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Correspondence to Pedro Hermosilla.

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Hermosilla, P., Krone, M., Guallar, V. et al. Interactive GPU-based generation of solvent-excluded surfaces. Vis Comput 33, 869–881 (2017). https://doi.org/10.1007/s00371-017-1397-2

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Keywords

  • Molecular visualization
  • Surface representation
  • Distance field