Molecular Dynamics Simulation
Program Overview
Bioinformatics
Structure of the target protein; 3D structure, active site, activity regulation, isoforms, annotation score, sequence length.
Introduction to MD simulations
- Mathematical concepts of coordinate systems, series expansion, vectors, matrix notations, and complex numbers.
- Potential energy and potential energy surface.
- Difference between statistical average and true average
- Basic statistical analysis to analyze MD trajectories.
Force Fields
- Bonded and nonbonded interactions.
- Periodic boundary conditions.
- Minimum image convention.
- Solvent effects.
MD simulation processing
- Running MD.
- Macroscopic variables.
- Monitoring equilibrium.
- MD analysis.
Running MD simulations and Data analysis
- Visualization using VMD 3 MD algorithms and solvent effects
- Setting up an MD simulation using NAMD.
- MD simulation processing.
MD simulation data analysis
- Analysis of MD simulations
- Data interpretation and presentation.
Drug binding interactions
- Enthalpic interactions.
- Entopic Interactions.
Predicting drug binding affinities
- End points methods.
- Alchemical modification methods.
- Path sampling methods.
MM-PBSA analysis
- Running the Amber MM-PBSA analysis using Amber tools.
Metadynamics and the free energy surface
- The sampling problem.
- Theory behind metadynamics.
Running Metadynamics
- Running Metadynamics using Gromacs.
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Duration: 10 weeks.
30-40 hours to complete.
- Level: Basic introductory and Advanced applications.
- Prerequisite: Basics of Organic Chemistry and Biology background is mandatory. Computer Science is preferred but not mandatory.
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Fee: 15 000 EGP
Discount Policy for Group Registration!
- Program timeframe:
- Registration
- Be contacted to confirm the participation
- Scheduling for the program sessions
- Supplied with the technical support to download the software required for the program