Fundamentals of molecular modelling
A two-day course on the basics of molecular modeling will provide participants with a comprehensive understanding of molecular dynamics simulation and molecular docking techniques. The participant will acquire the necessary knowledge and skills to perform basic MD simulations, analyze trajectories and conduct molecular docking studies in practical applications.
The course is designed to provide fundamental knowledge and skills in the field of molecular modeling, focusing on two fundamental techniques: molecular dynamics (MD) simulation and molecular docking.
The course is in English (or Polish – if the whole group of participants will be Polish-speaking).
Date and place
*Price includes: participation in classes, training materials, certificate of participation, coffee catering.
Molecular Dynamics Simulation
- Introduction to Molecular Dynamics (MD)
- What is MD and its importance in computational chemistry and biology?
- Popular force fields in computer simulations and their applications.
- Hands-on demonstration of running a simple MD simulation by using Gromacs software.
- Preparing input files and system parameters.
- Solvation and ionization of the system.
- Trajectory Analysis
- Analysis of MD trajectories.
Day 1 Milestones:
- Understanding the fundamental principles of Molecular Dynamics simulations.
- Hands-on experience of running a basic MD simulation.
- Basic knowledge of trajectory analysis.
- Introduction to Molecular Docking
- What is molecular docking and its significance in drug discovery and protein-ligand interactions?
- Docking Algorithms and Scoring Functions.
- Hands-on demonstration of running a simple molecular docking studies by using Autodock Vina software.
- Preparing receptor and ligand for docking studies.
- Visualization and analysis of docking results.
- Discussion of applications in drug discovery and protein-ligand interactions.
Day 2 Milestones:
- Understanding the principles and techniques of Molecular Docking.
- Hands-on experience in running a docking simulation.
- Knowledge of post-docking analysis and refinement techniques.
- Insight into practical applications of molecular docking.