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).
- Are you a student or researcher who knows that molecular modeling plays a key role in understanding the behavior of biological molecules and the interactions between proteins and ligands?
- Are you a drug discovery scientist who knows that molecular docking is a powerful tool used in drug discovery to predict how potential drug molecules bind to target proteins?
- Or maybe you are a computer scientist, bioinformatician, work in the biotechnology or pharmaceutical industry or are a self-taught person who wants to explore the application of their skills and would like to benefit from learning molecular modeling techniques.
- This course is for you!
*Price includes: participation in classes, training materials, certificate of participation, coffee catering.
Programme
Day 1.
Molecular Dynamics Simulation
Morning Session:
- 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.
Afternoon Session:
- 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.
Day 2.
Molecular Docking
Morning Session:
- Introduction to Molecular Docking
- What is molecular docking and its significance in drug discovery and protein-ligand interactions?
- Docking Algorithms and Scoring Functions.
Afternoon Session:
- 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.
- All attendees will receive a course completion certificate.
- Better together - get a 10% discount on the open course for each additional employee from your company.
