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    Molecular Docking

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    Anand Maurya
    This document provides an overview of molecular docking. It discusses how docking is used to predict the binding orientation of small molecule drugs to protein targets. The key interactions involved in docking are electrostatic, van der Waals, steric, solvent-related, and conformational changes. Docking algorithms search for binding configurations and scoring functions evaluate the strength of interactions. Common docking methods are lock-and-key and induced fit. Major steps in docking include building the receptor, identifying the active site, ligand preparation, and performing the docking simulation. Molecular docking has applications in virtual screening, drug discovery, and identifying protein-protein or protein-nucleotide interactions.

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    Molecular Docking

    Uploaded by

    Anand Maurya
    309 views13 pages
    This document provides an overview of molecular docking. It discusses how docking is used to predict the binding orientation of small molecule drugs to protein targets. The key interactions involved in docking are electrostatic, van der Waals, steric, solvent-related, and conformational changes. Docking algorithms search for binding configurations and scoring functions evaluate the strength of interactions. Common docking methods are lock-and-key and induced fit. Major steps in docking include building the receptor, identifying the active site, ligand preparation, and performing the docking simulation. Molecular docking has applications in virtual screening, drug discovery, and identifying protein-protein or protein-nucleotide interactions.

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    This document provides an overview of molecular docking. It discusses how docking is used to predict the binding orientation of small molecule drugs to protein targets. The key interactions involved in docking are electrostatic, van der Waals, steric, solvent-related, and conformational changes. Docking algorithms search for binding configurations and scoring functions evaluate the strength of interactions. Common docking methods are lock-and-key and induced fit. Major steps in docking include building the receptor, identifying the active site, ligand preparation, and performing the docking simulation. Molecular docking has applications in virtual screening, drug discovery, and identifying protein-protein or protein-nucleotide interactions.

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    © All Rights Reserved
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    Download as pptx, pdf, or txt
    309 views13 pages

    Molecular Docking

    Uploaded by

    Anand Maurya
    This document provides an overview of molecular docking. It discusses how docking is used to predict the binding orientation of small molecule drugs to protein targets. The key interactions involved in docking are electrostatic, van der Waals, steric, solvent-related, and conformational changes. Docking algorithms search for binding configurations and scoring functions evaluate the strength of interactions. Common docking methods are lock-and-key and induced fit. Major steps in docking include building the receptor, identifying the active site, ligand preparation, and performing the docking simulation. Molecular docking has applications in virtual screening, drug discovery, and identifying protein-protein or protein-nucleotide interactions.

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    You are on page 1of 13

    Molecular Docking

    Presented toDr. Pramod Yadav

    Presented byPiyush Pandey


    Bioinformatics
    13MTBINF006

    Introduction
    Docking attempts to find the best matching between two molecules
    Docking is frequently used to predict the binding orientation of small
    molecule drug to their protein targets.
    The small molecule called Ligand usually interacts with proteins
    binding sites.
    Binding sites are areas of protein known to be active in forming of
    compounds.
    The results of docking can be used to find inhibitors for specific target
    proteins and to design new drugs.

    Different types of Interactions


    Electrostatic forces - Forces with electrostatic origin are due to the
    charges residing in the matter. The most common interactions are
    charge-charge, charge-dipole and dipole-dipole.
    Electrodynamics forces-The most widely known is probably the van
    der Waals interaction. Van der Waals forces are driven by induced
    electrical interactions between two or more atoms or molecules that
    are very close to each other.
    Steric forces - Steric forces are caused by entropy. For example,
    in cases where entropy is limited, there may be forces to minimize
    the free energy of the system, which are due to entropy.

    Different types of Interactions


    Solvent-related forces - Solvent-related forces are due to the
    structural changes of the solvent. These structural changes are
    generated, when ions, colloids, proteins etc. are added into the
    structure of solvent. The most commonly are Hydrogen bond and
    hydrophobic interactions.
    conformational changes in the protein and the ligand are often
    necessary for a successful docking process

    Molecular docking can be divided into


    two separate sections.
    Search algorithm-The algorithm should create an optimum number
    of configurations that include the experimentally determined binding
    modes.
    Molecular dynamics
    Monte Carlo methods
    Genetic algorithms
    Fragment-based methods
    Distance geometry methods

    Scoring Function
    scoring functions are fast approximate mathematical methods used to
    predict the strength of the non-covalent interaction between two
    molecules after they have been docked.
    Scoring functions have also been developed to predict the strength of
    other types of intermolecular interactions.

    The following are majorly used method


    for docking
    1-Lock and Key Docking:-Here, the protein can be thought of as the
    lock and the ligand can be thought of as a key. find the correct
    relative orientation of the key which will open up the lock.
    2-Induced fit:-An enumeration on the rotations of one of the molecules
    is performed. Every rotation the surface cell occupancy and energy
    is calculated; later the most optimum pose is selected.

    Major steps in molecular docking:


    Building the ReceptorThis step the 3D structure of the receptor should be considered which
    can be downloaded from PDB; later the available structure should be
    processed.
    Identification of the Active Site
    the active site within the receptor should be identified. The receptor
    may have many active sites but the one of the interest should be
    selected. Most of the water molecules and heteroatom if present
    should be removed.

    Major steps in molecular docking:


    Ligand Preparation
    Ligands can be obtained from various databases like ZINC, PubChem
    or can be sketched using tools Chemsketch. While selecting the ligand,
    the LIPINSKYS RULE OF 5 should be applied.
    LIPINSKYS RULE: Not more than 5 H bond donors.
    Molecular Weight NOT more than 500 Da.
    Log P not over 5.
    NOT more than 10 H bond acceptors.

    Major steps in molecular docking:


    Docking
    This is the last step, where the ligand is docked onto the receptor
    and the interactions are checked. The scoring function generates
    score depending on which the best fit ligand is selected.

    Application

    Virtual screening
    Drug discovery
    Binding site identification
    Protein-protein or protein-nucleotide interaction.

    Software's for Molecular Docking:


    SANJEEVINI.
    SCHRODINGER
    DOCK
    AUTOLOCK TOOLS.
    DISCOVERY STUDIO.
    iGemDock

    Thank you

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