Course: Protein-Ligand Molecular Dynamics
Duration: 12 h (3 Saturdays)
Course start: January 8, 2022
Modality: Online synchronous / asynchronous
Spanish Language
about the course
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.
TEMARY
Unit I: Protein Basics (3 hours)
Protein
Proteins
Importance of proteins as biomolecules
Properties and classification of amino acids
Structural levels of proteins
Structure and function relationship in proteins
Unit II: Protein-Ligand Molecular Dynamics (6 hours)
Application of molecular dynamics for the study of biomolecules
Concepts on molecular dynamics
Definition of molecular dynamics
Methodology overview
Force field and parameters
Algorithms
Periodic conditions
Temperature and pressure controls
Introduction to the NAMD program
NAMD as a molecular dynamics package
NAMD Overview
Generation of the simulation system
Analysis of the initial structure
System load neutralization
Solvation of the simulation system
Establishment of the simulation routine
Description of the phases of a simulation algorithm
Generation of input files (inputs) for the simulation
Exercising to run a short dynamic
Protein-Ligand.
Unit III: Analysis of Molecular Dynamics (6 hours)
Simulation analysis with Carma
Introduction to Carma
Description of an input file
Calculation and analysis of root mean square deviation (RMSD)
Calculation and analysis of radius of gyration (RG)
Calculation and analysis of mean square fluctuation (RMSF)
Structure grouping
Calculation and Analysis of Principal Components (PCA)
Calculation of free energy of ligands in Molecular Dynamics
Analysis of protein-ligand dynamics data with VMD
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