Prof. Martin Zacharias
Molecular Dynamics Simulation of Biomolecules
My research group uses computer simulation methods to study the structure, function and dynamics of biomolecules and large biomolecular complexes. As the main computational technique we employ Molecular Dynamics simulations based on a force field to follow molecular motions including the surrounding solvent and ions. It allows us to better understand the molecular details of structure formation processes of proteins and nucleic acids and to extract thermodynamics properties. We apply these methods to study enzymes, amyloid structures and protein-protein interactions.
Our main research areas are:
- Analysis of protein-protein and protein-DNA interactions using Molecular Dynamics and Free Energy simulations
- Protein and peptide folding and amyloid structure formation
- Prediction and thermodynamics analysis of protein-ligand complex formation