Fundamentals of molecular modelling

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).

*Price includes: participation in classes, training materials, certificate of participation, coffee catering.


Day 1.

Predicting the 3D structure of a protein (AlphaFold2) and Molecular Docking

Morning Session:

Introduction to predicting the 3D structure of a protein – AlphaFold2 method.

Practical exercise 1:
Predicting the 3D structure of a protein by using AlphaFold2 method.

  1. Preparation for prediction – getting the amino acids sequence.
  2. Running Alphafold2.
  3. Comparing predicted structure with a known structure, using RMSD analysis.
  4. Short discussion about the results.

Lecture 2:

  1. Introduction to Molecular Docking.
  2. The significance of docking in drug discovery
  3. Docking algorithms and scoring functions.

Afternoon Session:

Practical exercise 2:
Molecular docking and result analysis.

  1. Obtaining structures of receptors and ligands.
  2. Preparation of protein and ligand structures.
  3. Generating possible ligand conformations and orientations relative to the protein.
  4. Evaluation of the ligand’s fit to the protein’s binding site using scoring functions.
  5. Ranking ligand conformations according to score values and selecting the best fitting ones, with the lowest protein-ligand interaction energy.
  6. Analysis of results: determining the orientation and binding position of the ligand as well as the amino acids relevant for protein-ligand interactions.

Day 1 milestones:

  1. Understanding the molecular docking method.
  2. Practical experience in conducting molecular docking of a protein-ligand complex.
  3. The ability to independently analyze molecular docking results.

Day 2.

Molecular Dynamics simulations


Morning Session:

Introduction to MD simulations and types of force fields in computer simulations.

Afternoon Session:

Practical exercise: MD simulation of a protein-ligand complex

  1. Preparation of initial protein and ligand structures for simulation.
  2. Define the unit cell and fill it with water.
  3. Adds ions to solvated system.
  4. Energy minimization.
  5. Equilibration.
  6. Production MD simulation.
  7. Analysis of results.

Day 2 milestones:

  1. Understanding the fundamental principles of MD simulations.
  2. Practical experience of running MD simulation.
  3. The ability to independently analysis of results.
Interested? Register now! Fill out the register form.