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

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Presentation on theme: "1st EELA-2 Grid School 2-15 November 2008. Jérôme Verleyen Juan Manuel Hurtado Rámirez Enrique Merino Pérez META-DOCK."— Presentation transcript:

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

2 Meta - Dock Introduction 2 What is Docking? But we are talking about proteins

3 Meta - Dock  Protein is a gen product. 3 DNAProtein Biological Process (Transcription, Traduction) What is a protein?

4 Meta - Dock 4 Proteins functions.  Regulators, defensives, catalyst, structure, etc. Example of protein regulator and pathways

5 Meta - Dock Disease example 5 Example pathways problems

6 Meta - Dock 6 How to block this protein? LIGAND

7 Meta - Dock 7 Now, what is Protein docking in silico

8 Meta - Dock 8 Now, what is Protein docking in silico Movie: by Autodock site

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

10 Meta - Dock 10 Step 1. Preparing protein receptor. Adding Hydrogen atomsAdding charges

11 Meta - Dock 11 Step 2. Grid parameter file. Defining area of grid

12 Meta - Dock Which ligands ? 12 Data Bases of ligands: - Free access. - Commercial access. By example free access for: ZINC. (8 millions of ligands) NCI Diversiy set.

13 Meta - Dock  Genetic algorithm Lamarckian:  Local search.  Simulated annealing. 13 Docking selection parameters.

14 Meta - Dock 14 Running virtual screening.  Calculate maps for each ligand’s atoms  Executing docking.  Analysis of results.

15 Meta - Dock 15 Analyzing results. Docked energy 226.96 Kcal/mol2120.96 Kcal/mol1690.96 Kcal/mol

16 Meta - Dock 16 Thanks to EELA project.

17 Meta - Dock Muito obrigado! 17 Questions

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