Article

TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes

Authors:

Chandrajit Bajaj,

Vinay Siddavanahalli,

Anthony ThaneAuthors Info & Claims

VIS '04: Proceedings of the conference on Visualization '04

Pages 243 - 250

https://doi.org/10.1109/VISUAL.2004.103

Published: 10 October 2004 Publication History

Abstract

While molecular visualization software has advanced over the years, today, most tools still operate on individual molecular structures with limited facility to manipulate large multi-component complexes. We approach this problem by extending 3D image-based rendering via programmable graphics units, resulting in an order of magnitude speedup over traditional triangle-based rendering. By incorporating a biochemically sensitive level-of-detail hierarchy into our molecular representation, we communicate appropriate volume occupancy and shape while dramatically reducing the visual clutter that normally inhibits higher-level spatial comprehension. Our hierarchical, image based rendering also allows dynamically computed physical properties data (e.g. electrostatics potential) to be mapped onto the molecular surface, tying molecular structure to molecular function. Finally, we present another approach to interactive molecular exploration using volumetric and structural rendering in tandem to discover molecular properties that neither rendering mode alone could reveal. These visualization techniques are realized in a high-performance, interactive molecular exploration tool we call TexMol, short for Texture Molecular viewer.

References

[1]

{1} Nataraj Akkiraju and Herbert Edelsbrunner. Triangulating the surface of a molecule. Discrete Appl. Math., 71(1-3):5-22, 1996.

Digital Library

[2]

{2} Daniel Aliaga, Jon Cohen, Andrew Wilson, Eric Baker, Hansong Zhang, Carl Erikson, Kenny Hoff, Tom Hudson, Wolfgang Stuerzlinger, Rui Bastos, Mary Whitton, Fred Brooks, and Dinesh Manocha. Mmr: an interactive massive model rendering system using geometric and image-based acceleration. In Proceedings of the 1999 symposium on Interactive 3D graphics, pages 199-206. ACM Press, 1999.

Digital Library

[3]

{3} Chandrajit L. Bajaj, Valerio Pascucci, Ariel Shamir, Robert J. Holt, and Arun N. Netravali. Dynamic maintenance and visualization of molecular surfaces. Discrete Applied Mathematics, 127(1):23-51, 2003.

Digital Library

[4]

{4} Nathan A. Baker, David Sept, Simpson Joseph, Michael J. Holst, and J. Andrew McCammon. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci., 98:10037- 10041, 2001.

[5]

{5} Chu-Fei Chang, Zhiyun Li, Amitabh Varshney, and Qiaode Jeffry Ge. Hierarchical image-based and polygon-based rendering for large-scale visualizations. Scientific Visualization, 2001.

[6]

{6} Michael L. Connolly. Analytical molecular surface calculation. Journal of Applied Crystallography, 16:548-558, 1983.

[7]

{7} Michael L. Connolly. Solvent-accessible surfaces of proteins and nucleic acids. Science, 221(4612):709-713, 1983.

[8]

{8} Lucia Darsa, Bruno Costa, and Amitabh Varshney. Walkthroughs of complex environments using image-based simplification. Computers and Graphics, 22(1):25-34, January 1998.

[9]

{9} Malcolm E. Davis and J. Andrew McCammon. Electrostatics in biomolecular structure and dynamics. Chem. Rev., 90:509-521, 1990.

[10]

{10} Paul E. Debevec, George Borshukov, and Yizhou Yu. Efficient view-dependent image-based rendering with projective texture-mapping. In 9th Eurographics Rendering Workshop, Vienna, Austria, June 1998.

[11]

{11} Warren L. DeLano. The pymol molecular graphics system. World Wide Web http://www.pymol.org, 2002.

[12]

{12} Huong Quynh Dinh, Ronald Metoyer, and Greg Turk. Real-time lighting changes for image-based rendering. IASTED International Conference on Computer Graphics and Imaging, 1998.

[13]

{13} Randima Fernando and Mark J. Kilgard. The Cg Tutorial: The Definitive Guide to Programmable Real-Time Graphics. Addison-Wesley Pub Co, February 2003.

Digital Library

[14]

{14} Thomas E. Ferrin, Conrad C. Huang, L. E. Jarvis, and Robert Langridge. The midas display system. Journal of Molecular Graphics, 6:13-27, 1988.

Digital Library

[15]

{15} David Gotz, Ketan Mayer-Patel, and Dinesh Manocha. Irw: An incremental representation for image-based walkthroughs. ACM Multimedia 2002, 2002.

Digital Library

[16]

{16} Andrew J. Hanson and Eric A. Wernert. Image-based rendering with occlusions via cubist images. In Proceedings of the conference on Visualization'98 , pages 327-334. IEEE Computer Society Press, 1998.

Digital Library

[17]

{17} Barry Honig and Anthony Nicholls. Classical electrostatics in biology and chemistry. Science, 268(1144-1149), 1995.

[18]

{18} William Humphrey, Andrew Dalke, and Klaus Schulten. VMD - Visual Molecular Dynamics. Journal of Molecular Graphics, 14:33-38, 1996.

[19]

{19} Stefan Jeschke and Michael Wimmer. Textured depth meshes for real-time rendering of arbitrary scenes. In Proceedings of the 13th Eurographics workshop on Rendering, pages 181-190. Eurographics Association, 2002.

Digital Library

[20]

{20} Andrew R. Leach. Molecular Modelling: Principles and Applications. Addison Wesley, 1996.

Digital Library

[21]

{21} Byungkook Lee and Frederic M. Richards. The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 55:379-400, 1971.

[22]

{22} Dong Hoon Lee and Soon Ki Jung. Capture configuration for image-based street walkthroughs. International Conference on Cyberworlds, 03-05:151, December 2003.

Digital Library

[23]

{23} Eric Martz. Protein explorer: Easy yet powerful macromolecular visualization. Trends in Biochemical Sciences, 27:107-109, February 2002. http://proteinexplorer.org.

[24]

{24} Nelson Max. Computer representation of molecular surfaces. IEEE Computer Graphics and Applications, pages 21-29, August 1983.

Digital Library

[25]

{25} Michel F. Sanner, Arthur J. Olson, and Jean-Claude Spehner. Fast and robust computation of molecular surfaces. In Proceedings of the eleventh annual symposium on Computational geometry, pages 406- 407. ACM Press, 1995.

Digital Library

[26]

{26} Michel F. Sanner, Arthur J. Olson, and Jean-Claude Spehner. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38(3):305-320, March 1996.

[27]

{27} Roger Sayle and E. James Milner-White. Rasmol: Biomolecular graphics for all. Trends in Biochemical Sciences (TIBS), 20(9):374, September 1995.

[28]

{28} Gernot Schaufler and Wolfgang Sturzlinger. A three dimensional image cache for virtual reality. Computer Graphics Forum (Eurographics'96) , 15(3):227-235, 1996.

[29]

{29} Amitabh Varshney and Frederick P. Brooks. Fast analytical computation of richards's smooth molecular surface. In Proceedings of the 4th conference on Visualization '93, pages 300-307, 1993.

Digital Library

[30]

{30} Richard Voorintholt, M. T. Kosters, G. Vegter, Gerrit Vriend, and Wim G. Hol. A very fast program for visualizing protein surfaces, channels and cavities. Journal of Molecular Graphics, 7(4):243-245, December 1989.

[31]

{31} John Westbrook and Paula M. Fitzgerald. Structural Bioinformatics, pages 161-179. P. E. Bourne and H. Weissig, John Wiley & Sons, Inc., 2003.

Cited By

Rasheed MClement NBhowmick ABajaj C(2019)Statistical Framework for Uncertainty Quantification in Computational Molecular ModelingIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.277124016:4(1154-1167)Online publication date: 1-Jul-2019
https://dl.acm.org/doi/10.1109/TCBB.2017.2771240
Rasheed MClement NBhowmick ABajaj C(2016)Statistical Framework for Uncertainty Quantification in Computational Molecular ModelingProceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2975167.2975182(146-155)Online publication date: 2-Oct-2016
https://dl.acm.org/doi/10.1145/2975167.2975182
Mwalongo FKrone MKarch GBecher MReina GErtl TPolys NChesnais AGobbetti EDöllner J(2014)Visualization of molecular structures using state-of-the-art techniques in WebGLProceedings of the 19th International ACM Conference on 3D Web Technologies10.1145/2628588.2628597(133-141)Online publication date: 8-Aug-2014
https://dl.acm.org/doi/10.1145/2628588.2628597
Show More Cited By

TexMol: Interactive Visual Exploration of Large Flexible Multi-Component Molecular Complexes
1. Applied computing
  1. Life and medical sciences
2. Theory of computation

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cover image ACM Conferences

VIS '04: Proceedings of the conference on Visualization '04

October 2004

667 pages

ISBN:0780387880

Sponsors

SIGGRAPH: ACM Special Interest Group on Computer Graphics and Interactive Techniques

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IEEE Computer Society

United States

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Published: 10 October 2004

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Cited By

Rasheed MClement NBhowmick ABajaj C(2019)Statistical Framework for Uncertainty Quantification in Computational Molecular ModelingIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.277124016:4(1154-1167)Online publication date: 1-Jul-2019
https://dl.acm.org/doi/10.1109/TCBB.2017.2771240
Rasheed MClement NBhowmick ABajaj C(2016)Statistical Framework for Uncertainty Quantification in Computational Molecular ModelingProceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2975167.2975182(146-155)Online publication date: 2-Oct-2016
https://dl.acm.org/doi/10.1145/2975167.2975182
Mwalongo FKrone MKarch GBecher MReina GErtl TPolys NChesnais AGobbetti EDöllner J(2014)Visualization of molecular structures using state-of-the-art techniques in WebGLProceedings of the 19th International ACM Conference on 3D Web Technologies10.1145/2628588.2628597(133-141)Online publication date: 8-Aug-2014
https://dl.acm.org/doi/10.1145/2628588.2628597
Parulek JJönsson DRopinski TBruckner SYnnerman AViola I(2014)Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular VisualizationComputer Graphics Forum10.1111/cgf.1234933:6(276-287)Online publication date: 1-Sep-2014
https://dl.acm.org/doi/10.1111/cgf.12349
Knoll AWald INavrátil PPapka MGaither K(2013)Ray tracing and volume rendering large molecular data on multi-core and many-core architecturesProceedings of the 8th International Workshop on Ultrascale Visualization10.1145/2535571.2535594(1-8)Online publication date: 17-Nov-2013
https://dl.acm.org/doi/10.1145/2535571.2535594
Liu FSong YLiu XXu XWang CMagnenat-Thalmann NPan Z(2013)Multi-layer screen-space ambient occlusion using hybrid samplingProceedings of the 12th ACM SIGGRAPH International Conference on Virtual-Reality Continuum and Its Applications in Industry10.1145/2534329.2534335(71-76)Online publication date: 17-Nov-2013
https://dl.acm.org/doi/10.1145/2534329.2534335
Bagur PShivashankar NNatarajan VTriggs BBala KChandran S(2012)Improved quadric surface impostors for large bio-molecular visualizationProceedings of the Eighth Indian Conference on Computer Vision, Graphics and Image Processing10.1145/2425333.2425366(1-8)Online publication date: 16-Dec-2012
https://dl.acm.org/doi/10.1145/2425333.2425366
Lipşa DLaramee RCox SRoberts JWalker RBorkin MPfister H(2012)Visualization for the Physical SciencesComputer Graphics Forum10.1111/j.1467-8659.2012.03184.x31:8(2317-2347)Online publication date: 1-Dec-2012
https://dl.acm.org/doi/10.1111/j.1467-8659.2012.03184.x
van der Zwan MLueks WBekker HIsenberg T(2011)Illustrative molecular visualization with continuous abstractionProceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization10.1111/j.1467-8659.2011.01917.x(683-690)Online publication date: 1-Jun-2011
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Zhao WXu GBajaj C(2011)An Algebraic Spline Model of Molecular Surfaces for Energetic ComputationsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2011.818:6(1458-1467)Online publication date: 1-Nov-2011
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