Overview
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Course content
Docking and HADDOCK
- Integrative modeling of biomolecular complexes
- HADDOCK tutorial
Molecular Dynamics Simulations
Simulation workflows with BioBB
- Simulation workflows with BioBB
- Tutorial – Protein-Complex MD Setup with Jupyter Notebooks and BioBB.
Introduction to QM/MM
- Introduction to QM/MM
- Tutorial – Introduction to QMMM simulations using GROMACS-CP2K Interface
Enhanced Sampling Methods
- Modeling molecular recognition through enhanced-sampling methods
- Tutorial – Metadynamics
Free energy calculations
- Introduction to alchemical free energy calculations using PMX
- Applications of alchemical free energy calculations
Trainer biographies
Technical help sheet
Further learning
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Integrative modeling of biomolecular complexes

Trainer: Alexandre Bonvin

Overview: These lectures cover the basics of docking. There is a specific focus on integrating experimental data into the experiments and on real applications of the tool.

Learning outcomes

By the end of this session you will be able to:

Explain the theory behind molecular docking
Describe how to integrate experimental data into your docking experiments
Give examples of docking applications.

Materials

Integrative modeling of biomolecular complexes – slides

Biomolecular simulations

Integrative modeling of biomolecular complexes