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Molecular Dynamics

Prof. Martin Zacharias

Research Field

The function of proteins and nucleic acids in living systems is strongly coupled to the molecular motion and dynamics of these biomolecules. Our group uses computer simulation methods to study the structure, function and dynamics of biomolecules. Our goal is to better understand structure formation processes and to elucidate the mechanism of ligand-receptor association in atomic detail. As the main computational technique we employ Molecular Dynamics simulations based on a classical force field to follow molecular motions including the surrounding solvent and ions. This allows us to extract thermodynamic and kinetic properties of the biomolecular system using methods of statistical mechanics. We also develop computational docking approaches to predict how proteins interact with other proteins or RNA and DNA molecules or how small drug-like compounds bind to biomolecular targets.

Address/Contact

James-Franck-Str. 1
85748 Garching b. München
+49 89 289 12393
Fax: +49 89 289 12444

Members of the Research Group

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Teaching

Course with Participations of Group Members

Offers for Theses in the Group

Role of DNA-deformability for recognition by proteins
Wie Protein an bestimmten Stellen entlang DNA spezifisch binden, ist noch nicht gut verstanden. In vielen Fällen scheint die mechanische Deformierbarkeit eine große Rolle zu spielen. Molekulardynamische Simulationen sollen eingesetzt werden, um den Beitrag der DNA-Flexibilität und Deformierbarkeit bei der Erkennung durch Proteine besser zu verstehen. Die Simulationen erlauben thermodynamische Beiträge, wie z.B. die freie Energie der DNA-Deformation, zu quantifizieren und ihren Beitrag an Modellsystemen zu analysieren.
suitable as
  • Bachelor’s Thesis Physics
  • Master’s Thesis Applied and Engineering Physics
Supervisor: Martin Zacharias

Current and Finished Theses in the Group

Role of DNA-deformability for recognition by proteins
Abschlussarbeit im Masterstudiengang Physics (Applied and Engineering Physics)
Themensteller(in): Martin Zacharias
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