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Introduction to Protein Docking: In Silico Approaches and Applications in Drug Discovery

This presentation provides an overview of protein docking, focusing on the biological significance of proteins and their functions. It explains the process of protein-ligand docking using in silico methods, highlighting tools like AutoDock. Key steps include preparing the protein receptor, creating grid parameter files, and virtual screening of ligands. Various docking parameters and algorithms are discussed to enhance docking accuracy. The presentation also addresses the analysis of docking results, emphasizing their implications in understanding diseases and developing therapeutic interventions.

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Introduction to Protein Docking: In Silico Approaches and Applications in Drug Discovery

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Presentation Transcript

  1. META-DOCK 1st EELA-2 Grid School Jérôme Verleyen Juan Manuel Hurtado Rámirez Enrique Merino Pérez 2-15 November 2008.

  2. Introduction What is Docking? But we are talking about proteins

  3. What is a protein? • Protein is a gen product. Biological Process (Transcription, Traduction) DNA Protein

  4. Proteins functions. • Regulators, defensives, catalyst, structure, etc. Example of protein regulator and pathways

  5. Disease example Example pathways problems

  6. How to block this protein? LIGAND

  7. Now, what is Protein docking in silico

  8. Now, what is Protein docking in silico Movie: by Autodock site

  9. How to do protein-ligand docking in silico. First application port to Grid : AutoDock The Scripps Research Institute http://autodock.scripps.edu/

  10. Step 1. Preparing protein receptor. Adding Hydrogen atoms Adding charges

  11. Step 2. Grid parameter file. Defining area of grid

  12. Whichligands? • Data Bases of ligands: • Free access. • Commercial access. • By example free access for: • ZINC. (8 millions of ligands) • NCI Diversiy set.

  13. Docking selection parameters. • Genetic algorithm Lamarckian: • Local search. • Simulated annealing.

  14. Running virtual screening. • Calculate maps for each ligand’s atoms • Executing docking. • Analysis of results.

  15. Analyzing results . Docked energy 226.96 Kcal/mol 2120.96 Kcal/mol 1690.96 Kcal/mol

  16. Thanks to EELA project.

  17. Muito obrigado! Questions

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