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Visual Haptic-Based Biomolecular Docking and Its Applications in E-Learning

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Transactions on Edutainment II

Part of the book series: Lecture Notes in Computer Science ((TEDUTAIN,volume 5660))

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Abstract

Visual haptic-based biomolecular docking systems could be used for both research and e-learning in research intensive disciplines such as biology, physical chemistry, molecular medicine, biophysics, structural biology, bioinformatics, etc. The assembly of molecules in a three-dimensional space or molecular docking is used for rational drug design where a ligand docks onto a receptor. The computer-aided design systems allow a real-time interactive visualization and manipulation of molecules in virtual environment. These techniques help the user to understand molecular interactions. In recent years, besides the visualization techniques, there has been increasing interest in using haptic interfaces to facilitate the exploration and analysis of molecular docking. Haptic device enables the users to manipulate the molecules and feel its interaction during the docking process in virtual experiment on computer. In this paper, we describe a visual haptic-based biomolecular docking system that we developed for research in helix-helix docking and propose its application in e-learning. We also describe haptic-based collaborative e-learning scenarios.

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References

  1. Martinez-Jimenez, P., Pontes-Pedrajas, A., Polo, J., Climent-Bellido, M.S.: Learning in Chemistry with Virtual Laboratories. J. Chemical Education 80(3), 346–352 (2003)

    Article  Google Scholar 

  2. Morozov, M., Tanakov, A., Gerasimov, A., Bystrov, D., Cvirco, E.: Virtual Chemistry Laboratory for School Education. In: Fourth IEEE International Conference on Advanced Learning Technologies (ICALT 2004), pp. 605–608 (2004)

    Google Scholar 

  3. Riganelli, A., Gervasi, O., Laganana, A., Alberti, M.: A Multiscale virtual reality approach to the chemical experiments. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J., Zomaya, A.Y. (eds.) ICCS 2003. LNCS, vol. 2658, pp. 324–330. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  4. Luo, Y., Guo, P., Hasegawa, S., Sato, M.: An Interactive Molecular Visualization System for Education in Immersive Multi-projection Virtual Environment. In: Third International Conference on Image and Graphics, Hong Kong, pp. 485–488. IEEE Computer Society Press, Los Alamitos (2004)

    Google Scholar 

  5. Sayle, R.A., Milner-White, E.J.: Rasmol: Biomolecular graphics for all. Trends in Biochemical Sciences (TIBS) 20(9), 374 (1995)

    Article  Google Scholar 

  6. DeLano, W.L.: The pymol molecular graphics system (2002), http://www.pymol.org

  7. Sourina, O., Korolev, N.: Geometric querying of time-dependent data for data mining in molecular dynamics. In: Proc. of Cyberworlds 2004, pp. 351–355. IEEE Press, Los Alamitos (2004)

    Chapter  Google Scholar 

  8. Sourina, O., Korolev, N.: Visual Mining and Spatio-Temporal Querying in Molecular Dynamics. The Journal of Computational and Theoretical Nanoscience 2(4), 492–498 (2005)

    Article  Google Scholar 

  9. Sankaranarayanan, G., Weghorst, S., Sanner, M., Gillet, A., Olson, A.: Role of haptics in teaching structural molecular biology. In: 11th Symposium on Haptic Interfaces for virtual Environments and Teleoperator Systems, pp. 363–366 (2003)

    Google Scholar 

  10. Davies, R.A., John, N.W., MacDonald, J.N., Hughes, K.H.: Visualization: Visualization of molecular quantum dynamics: a molecular visualization tools with integrated Web3D and haptics. In: 10th International Conf. on Web Technology Web3D 2005, pp. 143–150 (2005)

    Google Scholar 

  11. Persson, P.B., Cooper, M.D., Tibell, L.A.E., Ainsworth, S., Ynnerman, A., Jonsson, B.-H.: Designing and Evaluating a Haptic System for Biomolecular Education. In: IEEE Virtual Reality Conference, pp. 171–178 (2007)

    Google Scholar 

  12. JMol: an open-source Java viewer for chemical structures in 3D, http://jmol.sourceforge.net

  13. WebMO: free World Wide Web-based interface to computational chemistry packages with features for chemicals, crystals, materials and biomolecules, http://www.webmo.net

  14. WebMol: Java PDB Viewer, http://www.cmpharm.ucsf.edu/~walther/webmol.html

  15. FirstGlance in Jmol; A simple tool for macromolecular visualization, http://molvis.sdsc.edu/fgij/index.htm

  16. Lai-Yuen, S.K., Lee, Y.-S.: Interactive Computer-Aided Design for Molecular Docking and Assembly. Computer-Aided Design & Applications 3(6), 701–709 (2006)

    Article  Google Scholar 

  17. Liu, Q., Sourin, A.: Function-defined Shape Metamorphoses in Visual Cyberworlds. The Visual Computer 22(12), 977–990 (2006)

    Article  Google Scholar 

  18. Wei, L., Sourin, A., Sourina, O.: Function-based Haptic Interaction in Cyberworlds. In: 2007 International Conference on Cyberworlds, pp. 225–232. IEEE Press, Los Alamitos (2007)

    Chapter  Google Scholar 

  19. Wei, L., Sourin, A., Sourina, O.: Function-based visualization and haptic rendering in shared virtual spaces. The Visual Computer 24(10), 871–880 (2008)

    Article  Google Scholar 

  20. Sourina, O., Torres, J., Wang, J.: Visual Haptic-based Biomolecular Docking. In: 2008 International Conference on Cyberworlds, pp. 240–250. IEEE Press, Los Alamitos (2008)

    Chapter  Google Scholar 

  21. PDB - Protein Data Bank, Brookhaven National Laboratory, http://www.rcsb.org/pdb

  22. Bowie, J.U.: Helix packing in membrane proteins. J. Mol. Biol. 272(5), 780–789 (1997)

    Article  Google Scholar 

  23. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, A.C.G., Profeta Jr., S., Weiner, P.K.: A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765–784 (1984)

    Article  Google Scholar 

  24. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M.: CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Com. Chem. 4, 187–217 (1983)

    Article  Google Scholar 

  25. Lii, J.-H., Allinger, N.L.: The MM3 force field for amides, polypeptides and proteins. J. Comp. Chem. 12, 186–199 (1991)

    Article  Google Scholar 

  26. Allinger, N.L., Chen, K., Lii, J.-H.: An improved force field (MM4) for saturated hydrocarbons. J. Comp. Chem. 17, 642–668 (1996)

    Article  Google Scholar 

  27. Halgren, T.A.: Merck molecular force field. IV. Conformational energies and geometries. J. Comp. Chem. 17, 587–615 (1996)

    Google Scholar 

  28. Jorgensen, W.L., Maxwell, D.S., Tirado-Rives, J.: Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225–11236 (1996)

    Article  Google Scholar 

  29. Damm, W., Frontera, A., Tirado-Rives, J., Jorgensen, W.L.: OPLS all-atom force field for carbohydrates. J. Comp. Chem. 18, 1955–1970 (1997)

    Article  Google Scholar 

  30. Rizzo, R.C., Jorgensen, W.L.: OPLS all-atom model for amines: resolution of the amine hydration problem. J. Am. Chem. Soc. 121, 4827–4836 (1999)

    Article  Google Scholar 

  31. OPLS-aa force field parameter, http://egad.berkeley.edu/EGAD_manual/EGAD/examples/energy_function/ligands/oplsaa.txt (August 28, 2007)

  32. Martin, M.G.: Comparison of the AMBER, CHARMM, COMPASS, GROMOS, OPLS, TraPPE and UFF force fields for Prediction of vapor-liquid coexistence curves and liquid densities. Fluid Phase Equilib. 248, 50–55 (2006)

    Article  Google Scholar 

  33. Can, T., Chen, C.-I., Wang, Y.-F.: Efficient molecular surface generation using level-set methods. Journal of Molecular Graphics and Modelling 25(4), 442–454 (2006)

    Article  Google Scholar 

  34. Lorensen, W.E., Cline, H.E.: Marching Cubes: A high resolution 3D surface construction algorithm. Computer Graphics 21(4), 163–169 (1987)

    Article  Google Scholar 

  35. Yin, H., Slusky, J.S., Berger, B.W., Walters, R.S., Vilaire, G., Litvinov, R.I., Lear, J.D., Caputo, G.A., Bennett, J.S., DeGrado, W.F.: Computational Design of Peptides That Target Transmembrane Helices. Science 315, 1817–1822 (2007)

    Article  Google Scholar 

  36. Prasolova-Førland, E., Sourin, A., Sourina, O.: Place Metaphors in Educational Cyberworlds: a Virtual Campus Case Study. The Visual Computer 22(12), 1015–1028 (2006)

    Article  Google Scholar 

  37. Sourin, A., Sourina, O., Prasolova-Førland, E.: Cyber-learning in Cyberworlds. Journal of Cases on Information Technology 8(4), 55–70 (2006)

    Article  Google Scholar 

  38. Sourin, A., Sourina, O., Wei, L., Gagnon, P.: Visual Immersive Haptic Mathematics in Shared Virtual Spaces. In: Gavrilova, M.L., Tan, C.J.K. (eds.) Transactions on Computational Science III. LNCS, vol. 5300, pp. 1–19. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

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Author information

Authors and Affiliations

  1. Nanyang Technological University, Singapore

    Olga Sourina, Jaume Torres & Jing Wang

Authors
  1. Olga Sourina
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  2. Jaume Torres
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  3. Jing Wang
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Editor information

Editors and Affiliations

  1. State Key Lab of CAD&CG, Zhejiang University, 310027, Hangzhou, China

    Zhigeng Pan

  2. Mixed Reality Lab, National University of Singapore, Singapore

    Adrian David Cheok

  3. Media Education and Visualization Group, University of Education, Leibnizstr. 3, 88250, Weingarten, Germany

    Wolfgang Müller

  4. School of Computing, Liverpool John Moores University, Liverpool, UK

    Abdennour El Rhalibi

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Sourina, O., Torres, J., Wang, J. (2009). Visual Haptic-Based Biomolecular Docking and Its Applications in E-Learning. In: Pan, Z., Cheok, A.D., Müller, W., Rhalibi, A.E. (eds) Transactions on Edutainment II. Lecture Notes in Computer Science, vol 5660. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03270-7_8

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  • DOI: https://doi.org/10.1007/978-3-642-03270-7_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-03269-1

  • Online ISBN: 978-3-642-03270-7

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