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Docking techniques

D
Devika Rana

Docking is a computational method that predicts the preferred orientation of one molecule to another when bound to form a stable complex. It involves searching high-dimensional spaces to find the best matching between two molecules, such as a protein and ligand. Successful docking methods effectively search these spaces and use scoring functions to correctly rank candidate dockings in order to identify the correct ligand binding position and predict binding affinity.

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Docking Techniques
Introduction Docking is an attempt to find the best matching between two molecules. A more serious definition. Docking is a method which predicts the preferred orientation of one ligand when bound in an active site to form a stable complex. Finding the correct relative orientation of the key which will open up the lock. The protein can be thought of as the lock and the ligand can be thought of as a key.
Ligand in catalytic pocket Protein(Cysteine Protease) Protein with Ligand
Introduction Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings
Molecular Docking Molecular docking Identification of correct ligand binding Prediction of binding affinity Rational Drug Design
Types of Docking Rigid Docking (Lock and Key) In rigid docking, the internal geometry of both the receptor and ligand are treated as rigid. Flexible Docking (Induced fit) An enumeration on the rotations of one of the molecules (usually smaller one) is performed. Every rotation the energy is calculated; later the most optimum pose is selected.
Docking can be between. Protein Ligand Protein Protein Protein Nucleotide
Requirements Protein (Enzyme, peptide) Ligand (Drug, novel compound, testing compound, organic compound) Docking Software (Autodock) Result analysis
Target selection Protein preparation Docking Ligand selection Ligand preparation Docking Docking Result Evaluation Process of Molecular Docking Step:1 Step:2
Brutons tyrosine kinase inhibitors DOCKING DOCKING Screening of Compounds
SANJEEVINI IIT Delhi GOLD University of Cambridge ,UK AUTODOCK - Scripps Research Institute,USA GemDock(Generic Evolutionary Method for Molecular Docking) A tool, developed by Jinn-Moon Yang, a professor of the Institute of Bioinformatics, National Chiao Tung University, Taiwan Hex Protein Docking - University of Aberdeen, UK GRAMM (Global Range Molecular Matching) Protein docking - A Center for Bioinformatics, University of Kansas, USA Docking Software
Limitations(Pharmacophore & Docking) The major limitation in virtual screening by pharmacophore is the absence of good scoring metrics. Whereas docking simulations are based on scoring functions trying to predict the affinity, and similarity searches utilize similarity metrics. Pharmacophore queries do not have a reliable, general scoring metric. Most commonly, the quality of fitting the ligand into a pharmacophore query is expressed by the root mean square deviation between the features of the query and atoms of the molecule.
Application Pharmacophore approaches are successful subfields of computer-aided drug design (CADD) which have become one of the major tools hit identification lead optimization rational design of novel drugs. Virtual screening (hit identification) Drug Discovery (lead optimization) Bioremediation

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Docking techniques

  • 2. Introduction Docking is an attempt to find the best matching between two molecules. A more serious definition. Docking is a method which predicts the preferred orientation of one ligand when bound in an active site to form a stable complex. Finding the correct relative orientation of the key which will open up the lock. The protein can be thought of as the lock and the ligand can be thought of as a key.
  • 3. Ligand in catalytic pocket Protein(Cysteine Protease) Protein with Ligand
  • 4. Introduction Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings
  • 5. Molecular Docking Molecular docking Identification of correct ligand binding Prediction of binding affinity Rational Drug Design
  • 6. Types of Docking Rigid Docking (Lock and Key) In rigid docking, the internal geometry of both the receptor and ligand are treated as rigid. Flexible Docking (Induced fit) An enumeration on the rotations of one of the molecules (usually smaller one) is performed. Every rotation the energy is calculated; later the most optimum pose is selected.
  • 7. Docking can be between. Protein Ligand Protein Protein Protein Nucleotide
  • 8. Requirements Protein (Enzyme, peptide) Ligand (Drug, novel compound, testing compound, organic compound) Docking Software (Autodock) Result analysis
  • 10. Brutons tyrosine kinase inhibitors DOCKING DOCKING Screening of Compounds
  • 11. SANJEEVINI IIT Delhi GOLD University of Cambridge ,UK AUTODOCK - Scripps Research Institute,USA GemDock(Generic Evolutionary Method for Molecular Docking) A tool, developed by Jinn-Moon Yang, a professor of the Institute of Bioinformatics, National Chiao Tung University, Taiwan Hex Protein Docking - University of Aberdeen, UK GRAMM (Global Range Molecular Matching) Protein docking - A Center for Bioinformatics, University of Kansas, USA Docking Software
  • 12. Limitations(Pharmacophore & Docking) The major limitation in virtual screening by pharmacophore is the absence of good scoring metrics. Whereas docking simulations are based on scoring functions trying to predict the affinity, and similarity searches utilize similarity metrics. Pharmacophore queries do not have a reliable, general scoring metric. Most commonly, the quality of fitting the ligand into a pharmacophore query is expressed by the root mean square deviation between the features of the query and atoms of the molecule.
  • 13. Application Pharmacophore approaches are successful subfields of computer-aided drug design (CADD) which have become one of the major tools hit identification lead optimization rational design of novel drugs. Virtual screening (hit identification) Drug Discovery (lead optimization) Bioremediation