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Molecular Docking Using GOLD

Molecular Docking Using GOLD. Tommi Suvitaival Seppo Virtanen S-114.2500 Basics for Biosystems of the Cell Fall 2006. What is molecular docking?. How a flexible ligand binds to a protein Ligand Small molecule compared to the protein Protein A macromolecule

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Molecular Docking Using GOLD

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  1. Molecular Docking Using GOLD Tommi Suvitaival Seppo Virtanen S-114.2500 Basics for Biosystems of the Cell Fall 2006

  2. What is molecular docking? • How a flexible ligand binds to a protein • Ligand • Small molecule compared to the protein • Protein • A macromolecule • Might have an active site onto which the ligand attaches

  3. Interactions between the cyclic urea inhibitor and HIV-1 protease

  4. What is molecular docking? (2) • Difficult to predict • Parameters to be considered: • Hydrogen bonds, lipophilic properties, van der Waals interactions • Possible metal ions • Tensions of the ligand backbone • Conformation

  5. GOLD • ’Genetic Optimization for Ligand Docking’ • Input: • Exact protein and ligand configurations in order to get good results • Demand for other programs specialized in molecular visualization

  6. Genetic algorithm search method used to search the different binding modes of the ligands • The binding mode has geometric and chemical components • Docked ligands ranked by fitness score • Fitness functions

  7. Several possible conformations depicted in one picture

  8. Fitness functions • For determining the rank between possible geometries • Two choices: GoldScore or ChemScore • Different parameters used • Calculations based on chemical and physical theories • Geometrical properties • Bonding affinities

  9. Genetic algorithm • Initially a population of conformations is generated • Scoring algorithm evaluates the fitness of each conformation • conformation=chromosome • Genetic operations occur • Crossing-over • Fit members of the population crossover and replace the worst member of the population • Migration • Mutation

  10. Individual with the best properties is the result Highest rank

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