Docking Methodologies and Recent Advances

Docking Methodologies and Recent Advances

Ashwani Kumar (Guru Jambheshwar University of Science and Technology, India), Ruchika Goyal (Guru Jambheshwar University of Science and Technology, India) and Sandeep Jain (Guru Jambheshwar University of Science and Technology, India)
DOI: 10.4018/978-1-5225-0115-2.ch012
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Abstract

Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
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Fundamental Necessities

Molecular docking program emphasize on the following basic requirements (Mahajan, & Gill, 2014; Krovat, Steindl, & Langer, 2005):

  • 1.

    A target protein structure with or without a bound ligand is detected by various experimental techniques like NMR or X-Ray crystallography, but if protein structure is not present then protein prediction is done by any technique like threading modelling, homology modelling.

  • 2.

    Database containing existing or virtual compounds for the docking process

  • 3.

    Sampling and scoring method, desired scoring and searching algorithms require a computational framework for its efficient working

  • 4.

    The three-dimensional structure of the protein ligand complex has to be studied in depth of atomic resolution.

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