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
Ernst-Otto-Fischer-Straße 8/I
85748 Garching b. München
+49 89 289 12393
Fax: +49 89 289 12444
Members of the Research Group
Professor
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
Prof. Dr. | Martin | Zacharias | 046 | +49 89 289-12335 |
Office
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
Sonja | Ortner | 047 | +49 89 289-12393 |
Scientists
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
M.Sc. | Shu-Yu | Chen | 042 | +49 89 289-12564 | ||
M.Sc. | Maximilian | Kienlein | 044 | +49 89 289-12730 | ||
Brianda | Lopez Santini | 045 | +49 89 289-12731 | |||
Dr. | Patrick | Quoika | 048 | +49 89 289-13766 | ||
Dr. | Maria | Reif | 045 | +49 89 289-12731 | ||
M.Sc. | Carlos Christian | Sustay Martinez | 040 | +49 89 289-51612 | ||
M.Sc. | Luis | Vollmers | 044 | +49 89 289-12730 | ||
M.Sc. | Paul | Westphälinger | 044 | +49 89 289-12730 | ||
Dr. | Gabriel | Zoldak | 130 | – | ||
M.Sc. | Richard | Zschau | 042 | +49 89 289-12564 |
Students
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
B.Sc. | Maximilian | Block | – | – | ||
Asha | Knipp | – | – | |||
B.Sc. | Pawel | Korzeb | – | – | ||
B.Sc. | Mira Tanja | Mahlein | – | – | ||
B.Sc. | Yasmin | Saremi Nanji | – | – | ||
Luis Jakob | Walter | – | – | |||
Ziyi | Wang | – | – |
Other Staff
Photo | Degree | Firstname | Lastname | Room | Phone | |
---|---|---|---|---|---|---|
Dr. | Jonathan | Coles | 048 | – | ||
Susmita | De | – | – | |||
M.Sc. | Christina | Frost | – | – | ||
Margrethe | Gaardlos | – | – | |||
Ameya | Harmalkar | – | – | |||
M.Sc. | Julian | Hartmann | 701 | – | ||
Dr. | Manuel | Hitzenberger | 048 | +49 89 289-13766 | ||
Dr. | Korbinian | Liebl | – | +49 89 289-13697 | ||
Anshuman J. | Mahapatra | – | – | |||
M.Sc. | Danial | Pour Jafar Dehkordi | 059 | – | ||
B.Sc. | Arrien Symon | Rauh | – | – | ||
Jose | Roldan | – | – | |||
Prof. Dr. | Philipp | Scherer | 073 | – | ||
Neelanjana | Sengupta | – | – | |||
Till | Siebenmorgen | 059 | – |
Teaching
Course with Participations of Group Members
Current and Finished Theses in the Group
- Additive Beiträge zur Hydrations-Thermodynamik kleiner Moleküle: Ein Vergleich zwischen Molekulardynamik-Simulationen im expliziten Solvent und Kontinuum-Modellen
- Abschlussarbeit im Bachelorstudiengang Physik
- Themensteller(in): Martin Zacharias
- Aβ₉₋₄₀ Protofilament Association: Advanced Binding Free Energy Calculation and Thermodynamic Aspects
- Abschlussarbeit im Masterstudiengang Biophysik
- Themensteller(in): Martin Zacharias
- Accelerating Protein-Protein Docking Calculations using Graphics Processing Units
- Abschlussarbeit im Masterstudiengang "Applied and Engineering Physics"
- Themensteller(in): Martin Zacharias
- On the development of problem-oriented knowledge-based scoring functions for protein-protein docking
- Abschlussarbeit im Masterstudiengang Biophysik
- Themensteller(in): Martin Zacharias