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Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

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Abstract

Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called “pathway docking” in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

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Acknowledgments

The work was funded by the Institute for Computational Science and Technology at the Ho Chi Minh City. The authors gladly thank Hung Nguyen for helpful discussions.

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Authors and Affiliations

  1. Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam

    Diem-Trang T. Tran, Ly T. Le & Thanh N. Truong

  2. School of Biotechnology, International University, Ho Chi Minh City, Vietnam

    Ly T. Le

  3. Department of Chemistry, University of Utah, Salt Lake City, UT, USA

    Thanh N. Truong

Authors
  1. Diem-Trang T. Tran
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  2. Ly T. Le
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  3. Thanh N. Truong
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Correspondence to Thanh N. Truong.

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Tran, DT.T., Le, L.T. & Truong, T.N. Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase. J Comput Aided Mol Des 27, 689–695 (2013). https://doi.org/10.1007/s10822-013-9675-1

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  • DOI: https://doi.org/10.1007/s10822-013-9675-1

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