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Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK)

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Abstract

Understanding the principles of protein receptor recognition, interaction, and association with molecular substrates and inhibitors is of principal importance in the drug discovery process. MOLSDOCK is a molecular docking method that we have recently developed. It uses mutually orthogonal Latin square sampling (together with a variant of the mean field technique) to identify the optimal docking conformation and pose of a small molecule ligand in the appropriate receptor site. Here we report the application of this method to simultaneously identify both the low energy conformation and the one with the best pose in the case of 62 protein-bound nucleotide ligands. The experimental structures of all these complexes are known. We have compared our results with those obtained from two other well-known molecular docking software, viz. AutoDock 4.2.3 and GOLD 5.1. The results show that the MOLSDOCK method was able to sample a wide range of binding modes for these ligands and also scores them well.

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Acknowledgments

We thank the University Grants Commission, and the Department of Science and Technology, Government of India for support under the Centre of Advanced Study (CAS) program and the Fund for Improvement of S&T Infrastructure (FIST) program, respectively.

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Authors and Affiliations

  1. C.A.S. in Crystallography and Biophysics, University of Madras, Maraimalai Campus (Guindy), Chennai, 600025, India

    Shankaran Nehru Viji, Nagarajan Balaji & Namasivayam Gautham

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  1. Shankaran Nehru Viji
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  2. Nagarajan Balaji
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  3. Namasivayam Gautham
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Correspondence to Namasivayam Gautham.

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Viji, S.N., Balaji, N. & Gautham, N. Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK). J Mol Model 18, 3705–3722 (2012). https://doi.org/10.1007/s00894-012-1369-4

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  • DOI: https://doi.org/10.1007/s00894-012-1369-4

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