Workshop 4: Molecular Docking and Molecular Dynamics
Pr. Noureddine Tchouar
University of Sciences and Technology of Oran - USTO
Noureddine Tchouar is currently a professor at the University of Sciences and technology of Oran. He received his PhD degrees in Chemical Physics from University of Sciences and technology of Oran. His research interests cover the areas of chemistry physics and computational chemistry. He studies the quantum properties of dense fluids with molecular dynamics simulation and recently his main interest is to develop QSAR models of biomolecules by means of theoretical and computational methods.
Abstract:
Molecular docking is a method that predicts the preferred orientation of one molecule to another from a stable complex for example enzyme-substrate complex. This is so important to study the preferred orientation of the molecules and may be used to predict the strength of association or binding affinity. This can be achieved using computer-aided molecular docking to create a reasonably accurate model of energy and must be able to deal with the combinatorial complexity incurred by the molecular flexibility of the docking partners. Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules, throughout which we use enzymesenzyme as a model to define N-body simulation. The atoms and molecules are allowed to interact for a fixed period of time (nanosecond) giving a view of the dynamical evolution of the system. We will use program visualization ٍ(VMD)) to describe the fundamental aspect of analysis and data interpretation.
Outline
Introduction to the drug discovery process.
Molecular docking and quantum mechanics, a combined mechanistic tool
Modeling ligand–protein interactions in drug design.
Biological complexes and quaternary structures, the protein-ligand docking approach.
Solvent effect as an important parameter.
Molecular dynamics, Monte Carlo Method Simulation.
Atoms, molecules, chemistry.
Continuum modeling approaches and solution approaches.
Visualization and data analysis.
Biological systems (simulation in biophysics) how proteins do they work and how to model them.
Workshop - Molecular Docking : Dr. Sofiane BENMENTIR (USTO)
Optimization of 3D structure.
Principles of molecular docking.
Molecular docking simulation
a. Protein and ligand preparation for docking.
b. Docking simulation and analysis.
c. Visualization and H-bonds analysis.
Workshop- Molecular Dynamics (MD) : Dr. Sofiane BENMENTIR (USTO)
Principles of molecular dynamics.
System preparation and sitting up molecular dynamics simulation.
Molecular dynamics simulation
a.Introduction to analysis tools for MD simulation and analysis of MD trajectory.
b. Molecular visualization using pymol and VMD.
c. Analysis of MD trajectory.
Software
- AutoDock4 for molecular docking
- NAMD for molecular dynamics simulation
-Pymol and VMD for molecular visualization.
Keywords
Techniques: Molecular Docking, Molecular Dynamics Simulation, Virtual Screening, Interaction.
Others: Flexible docking