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International Conference on Artificial Reality and Telexistence

ICAT 2006: Advances in Artificial Reality and Tele-Existence pp 324–333Cite as

A Collaborative Virtual Reality Environment for Molecular Modeling

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Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 4282))

Abstract

A collaborative molecular modeling environment based on virtual reality techniques is proposed in this paper. The environment consists of a VR based molecular modeling system (VRMMS), a distributed processing system (DPS) and a web service server (WSS). The proposed environment was evaluated in terms of accuracy, performance, and collaboration. The accuracy of the simulation was examined by comparing the simulation results with those produced by the most popular simulation tool, Insight II. The distributed processing system of 4 computers showed good computing performance. The collaborative works of molecular modeling were successfully exercised and the total processing time of the collaboration was 3 times faster than that of a single user’s performance.

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References

  1. Pertuz, M.F., Rossmann, M.G., Cullis, A.F., Muirhead, H., Will, G., North, A.C.T.: Structure of myoglobin: A three-dimensional Fourier synthesis at 5.5 Angstrom resolution, obtained by X-ray analysis. Nature 185, 416–422 (1960)

    Article  Google Scholar 

  2. Wuethrich: NMR of Proteins and Nucleic Acids. John Wiley & Sons, Chichester (1986)

    Google Scholar 

  3. Richards, F.M.: Areas, volumes, packing and protein structures. Annual Review of Biophysics and Bioengineering 6, 151–176 (1977)

    Article  Google Scholar 

  4. RASMOL, http://www.umass.edu/rasmol

  5. Protein Explorer, http://www.umass.edu/micobio/chime/index.html

  6. Brooks Jr., F.P., Ouh-Young, M., Better, J.J., Kilpatrick, P.J.: Project GROPE-Haptic Display for Scientific Visualization. ACM Computer Graphics 24, 177–185 (1990)

    Article  Google Scholar 

  7. Humphrey, W., Dalke, A., Schulten, K.: VMD – Visual Molecul ar Dynamics. Journal of Molecular Grahpics 14, 33–38 (1996), http://www.ks.uiuc.edu/Research/vmd/

    Article  Google Scholar 

  8. Brooks, B.R., Bruccoleri, R.E., Olasfson, B.D., States, D.J., Swaminathan, S., Karplus, M.: CHARMM: A Promgram for Macromolecualr Energy Minimization, and Dynamics Calculations. J. Comp. Chem 4, 187 (1983)

    Article  Google Scholar 

  9. Kale, L.V., Bhandarkar, M., Brunner, R., Krawetz, N., Phillips, J., Shinozaki, A.: NAMD: A Case Study in Multilingual Parallel Programming. In: The 10th International Workshop on Languages and Compilers for Parallel Computing, pp. 367–381.

    Google Scholar 

  10. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Bilol. 215, 403–410 (1990)

    Article  Google Scholar 

  11. Bhandarkar, M., Budescu, G., Humphrey, W.F., Izaguirre, J.A., Izrailev, S., Kale, L.V., Kosztin, D., Molnar, F., Phillips, J.C., Schulten, K.: BioCoRE: A Collaboratory for Structural Biology. In: Bruzzone, A.G., Uchrmacher, A., Page, E.H. (eds.) Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, San Francisco, California, pp. 242–251 (1999)

    Google Scholar 

  12. Park, S., Lee, J., Kim, J.-I.: A Molecular Modeling System based on Dynamic Gesture. In: Gervasi, O., Gavrilova, M.L., Kumar, V., Laganá, A., Lee, H.P., Mun, Y., Taniar, D., Tan, C.J.K. (eds.) ICCSA 2005. LNCS, vol. 3480, pp. 886–895. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  13. Park, S., Kim, B., Kim, J.-I.: A Web Service based Molecualr Modeling System using a Distributed Processing System. In: Shimojo, S., Ichii, S., Ling, T.-W., Song, K.-H. (eds.) HSI 2005. LNCS, vol. 3597, pp. 208–217. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  14. Lee, J., Park, S., Kim, J.-I.: Adaptive Real-Time Rendering for Large-Scale Molecular Models. In: ISVC 2006 (2006)

    Google Scholar 

  15. Rutenber, E., Fauman, E.B., Keenan, R.J., Fong, S., Furth, P.S., de Montellano, P.R.O., Meng, E., Kuntz, I.D., De Camp, D.L., Salto, R., Rose, J.R., Craik, C.S., Stroud, R.M.: Structure of a Non-peptide Inhibitor Complexed with HIV-1 Protease. The Journal of Biological, Chemistry 268(21), 15343–15346 (1993)

    Google Scholar 

  16. Yasui-Furukori, N., Inoue, Y., Chiba, M., Tateishi, T.: Simultaneous determination of haloperidol and bromperidol and their reduced metabolites by liquid- liquid extraction and automated column-switching high-performance liquid chromatography. Journal of Chromatography B 805, 174–180 (2004)

    Article  Google Scholar 

  17. Wang, J., Morin, P., Wang, W., Kollman, P.A.: Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA. Journal of American Chemical Society 123, 5221–5320 (2001)

    Article  Google Scholar 

  18. Insight II, http://www.Accelrys.com

  19. http://en.wikipedia.org/wiki/Receptor_biochemistry

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Author information

Authors and Affiliations

  1. Game Engineering, Hoseo University, Cheonan, Korea

    Sungjun Park

  2. Computer Science & Engineering, Konkuk University, Seoul, Korea

    Jun Lee

  3. CAESIT, Konkuk University, Seoul, Korea

    Jee-In Kim

Authors
  1. Sungjun Park
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  2. Jun Lee
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  3. Jee-In Kim
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Editor information

Editors and Affiliations

  1. State Key Lab of CAD and CG, Zhejiang University, Hangzhou, P.R. China

    Zhigeng Pan

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

    Adrian Cheok

  3. Upper Austria University of Applied Science and Digital Media, Hagenberg, Austria

    Michael Haller

  4. Department of Computer Science, University of Durham, South Road, DH1 3LE, Durham, UK

    Rynson W. H. Lau

  5. Graduate School of Science and Technology, Keio University, 3-14-1 Hiyoshi Kohoku-ku, 223-8522, Yokohama, Japan

    Hideo Saito

  6. College of Information Engineering, Zhejiang University of Technology, 310032, Hangzhou, P.R. China

    Ronghua Liang

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© 2006 Springer-Verlag Berlin Heidelberg

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Park, S., Lee, J., Kim, JI. (2006). A Collaborative Virtual Reality Environment for Molecular Modeling. In: Pan, Z., Cheok, A., Haller, M., Lau, R.W.H., Saito, H., Liang, R. (eds) Advances in Artificial Reality and Tele-Existence. ICAT 2006. Lecture Notes in Computer Science, vol 4282. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11941354_33

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  • DOI: https://doi.org/10.1007/11941354_33

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-49776-9

  • Online ISBN: 978-3-540-49779-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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