1st EELA-2 Grid School

1st EELA-2 Grid School 2-15 November 2008.

Jérôme Verleyen

Juan Manuel Hurtado Rámirez

Enrique Merino Pérez

META-DOCK

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Introduction

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What is Docking?

But we are talking about proteins

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Protein is a gen product.

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DNA Protein

Biological Process (Transcription, Traduction)

What is a protein?

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Proteins functions. Regulators, defensives, catalyst, structure, etc.

Example of protein

regulator and pathways

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Disease example

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Example pathways problems

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How to block this protein?

LIGAND

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Now, what is Protein docking in silico

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Now, what is Protein docking in silico

Movie: by Autodock site

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How to do protein-ligand docking in silico.

First application port to Grid :

http://autodock.scripps.edu/

AutoDockThe Scripps Research Institute

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Step 1. Preparing protein receptor.

Adding Hydrogen atoms Adding charges

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Step 2. Grid parameter file.

Defining area of grid

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Which ligands?

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Data Bases of ligands:

- Free access.- Commercial access.

By example free access for:ZINC. (8 millions of ligands)NCI Diversiy set.

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Genetic algorithm Lamarckian: Local search. Simulated annealing.

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Docking selection parameters.

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Running virtual screening.

Calculate maps for each ligand’s atoms

Executing docking.

Analysis of results.

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Analyzing results .

Docked energy

226.96 Kcal/mol 2120.96 Kcal/mol 1690.96 Kcal/mol

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Thanks to EELA project.

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Muito obrigado!

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Questions