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GVSS: A High Throughput Drug Discovery Service of Avian Flu and Dengue Fever for EGEE and EUAsiaGrid

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Abstract

In the study of Biomedicines, molecular docking simulation is a common method for predicting potential interacting complexes of small molecules in protein binding sites. However, it is a time-consuming process to search exhaustively all correct conformations of a compound. This study demonstrates how massive molecular docking benefit from state-of-the-art Grid technology. Providing intensive computing power and effective data management, the production e-infrastructure (such as EGEE and EUAsiaGrid) enables opportunities for in-silico drug discovery on the neglected and emerging diseases, for instance, avian influenza and dengue fever. In this study, Grid Application Platform (GAP) and GAP-enabled Virtual Screening Service (GVSS) were developed with the docking engine of the Autodock 3.0.5. A JAVA-based graphical user interface and the GAP allow end-users to specify target and compound library, set up docking parameters, monitor docking jobs and computing resources, visualize and refine docking results, and finally download the final results. To provide a more user-friendly Grid service, GVSS was designed for conducting large-scale molecular docking more easily.

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Authors and Affiliations

  1. Research Center for Information Technology Innovation, Academia Sinica, 128, Sec. 2, Academia Rd., Nankang, Taipei, 115, Taiwan

    Hsin-Yen Chen, Mason Hsiung & Eric Yen

  2. The National Institute for Nuclear Physics and High Energy Physics (NIKHEF), Science Park 105, 1098 XG, Amsterdam, The Netherlands

    Hurng-Chun Lee

  3. Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Rd., Nankang, Taipei, 115, Taiwan

    Simon C. Lin

  4. Genomics Research Center, Academia Sinica, 128, Sec. 2, Academia Rd., Nankang, Taipei, 115, Taiwan

    Ying-Ta Wu

Authors
  1. Hsin-Yen Chen
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  2. Mason Hsiung
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  3. Hurng-Chun Lee
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  4. Eric Yen
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  5. Simon C. Lin
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  6. Ying-Ta Wu
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Corresponding authors

Correspondence to Simon C. Lin or Ying-Ta Wu.

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Chen, HY., Hsiung, M., Lee, HC. et al. GVSS: A High Throughput Drug Discovery Service of Avian Flu and Dengue Fever for EGEE and EUAsiaGrid. J Grid Computing 8, 529–541 (2010). https://doi.org/10.1007/s10723-010-9159-7

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  • DOI: https://doi.org/10.1007/s10723-010-9159-7

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