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MDock: A Suite for Molecular Inverse Docking and Target Prediction

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Protein-Ligand Interactions and Drug Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2266))

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Abstract

Molecular docking is commonly used for identification of drug candidates targeting a specified protein of known structure. With the increasing emphasis on drug repurposing over recent decades, molecular inverse docking has been widely applied to prediction of the potential protein targets of a specified molecule. In practice, inverse docking has many advantages, including early supervision of drugs’ side effects and toxicity. MDock developed from our laboratory is a protein–ligand docking software based on a knowledge-based scoring function and has numerous applications to lead identification. In addition to its computational efficiency on ensemble docking for multiple protein conformations, MDock is well suited for inverse docking. In this chapter, we focus on introducing the protocol of inverse docking with MDock. For academic users, the MDock package is freely available at http://zoulab.dalton.missouri.edu/mdock.htm.

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Acknowledgments

Support to XZ from OpenEye Scientific Software Inc. (Santa Fe, NM, http://www.eyesopen.com) is gratefully acknowledged. This work was supported by NIH grants R01GM109980 (PI: XZ), R35GM136409 (PI: XZ), R01HL126774 (PI: Jianmin Cui), and R01HL142301 (PI: Jonathan Silva) to XZ. The computations were performed on the high performance computing infrastructure supported by NSF CNS-1429294 (PI: Chi-Ren Shyu) and the HPC resources supported by the University of Missouri Bioinformatics Consortium (UMBC).

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Authors and Affiliations

  1. Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA

    Zhiwei Ma & **aoqin Zou

Authors
  1. Zhiwei Ma
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  2. **aoqin Zou
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Correspondence to **aoqin Zou .

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Editors and Affiliations

  1. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Flavio Ballante

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Ma, Z., Zou, X. (2021). MDock: A Suite for Molecular Inverse Docking and Target Prediction. In: Ballante, F. (eds) Protein-Ligand Interactions and Drug Design. Methods in Molecular Biology, vol 2266. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1209-5_18

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  • DOI: https://doi.org/10.1007/978-1-0716-1209-5_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1208-8

  • Online ISBN: 978-1-0716-1209-5

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