This course will allow you to learn concepts about protein structure, ligands, force fields, and non-covalent protein-ligand interactions, conformational changes, prepare your system to run protein-ligand molecular dynamics, run your simulation, analyze your results as rmsd, Rg , rmsf, non-covalent protein-ligand interactions, calculated energy, etc.

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TEMARY

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Unit I: Protein Basics (3 hours)

1. Protein

   1. Proteins

   2. Importance of proteins as biomolecules

   3. Properties and classification of amino acids

   4. Structural levels of proteins

   5. Structure and function relationship in proteins

Unit II: Protein-Ligand Molecular Dynamics (6 hours)

1. Application of molecular dynamics for the study of biomolecules

2. Concepts on molecular dynamics

   1. Definition of molecular dynamics

   2. Methodology overview

   3. Force field and parameters

   4. Algorithms

   5. Periodic conditions

   6. Temperature and pressure controls

3. Introduction to the NAMD program

1. NAMD as a molecular dynamics package

   1. NAMD Overview

   2. Generation of the simulation system

   3. Analysis of the initial structure

   4. System load neutralization

   5. Solvation of the simulation system

   6. Establishment of the simulation routine

   7. Description of the phases of a simulation algorithm

   8. Generation of input files (inputs) for the simulation

   9. Exercising to run a short dynamic

2. Protein-Ligand.

Unit III: Analysis of Molecular Dynamics (6 hours)

1. Simulation analysis with Carma

2. Introduction to Carma

   1. Description of an input file

   2. Calculation and analysis of root mean square deviation (RMSD)

   3. Calculation and analysis of radius of gyration (RG)

   4. Calculation and analysis of mean square fluctuation (RMSF)

   5. Structure grouping

   6. Calculation and Analysis of Principal Components (PCA)

   7. Calculation of free energy of ligands in Molecular Dynamics

3. Analysis of protein-ligand dynamics data with VMD

Do you want more to know more about the agenda? Download the PDF version