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 | |
|---|---|---|---|---|---|---|
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Prof. Dr. | Martin | Zacharias | EG.046 | +49 89 289-12335 |
Office
| Photo | Degree | Firstname | Lastname | Room | Phone | |
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Sonja | Ortner | EG.047 | +49 89 289-12393 |
Scientists
| Photo | Degree | Firstname | Lastname | Room | Phone | |
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M.Sc. | Shu-Yu | Chen | EG.042 | +49 89 289-12564 | |
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Dr. | Manuel | Hitzenberger | EG.048 | +49 89 289-13766 | |
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M.Sc. | Maximilian | Kienlein | EG.044 | +49 89 289-12730 | |
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Brianda | Lopez Santini | EG.045 | +49 89 289-12731 | ||
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Dr. | Patrick | Quoika | EG.048 | +49 89 289-13766 | |
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Dr. | Maria | Reif | EG.045 | +49 89 289-12731 | |
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M.Sc. | Luis | Vollmers | EG.044 | +49 89 289-12730 | |
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M.Sc. | Paul | Westphälinger | EG.044 | +49 89 289-12730 | |
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Dr. | Gabriel | Zoldak | 3130 | – | |
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M.Sc. | Richard | Zschau | EG.042 | +49 89 289-12564 |
Students
| Photo | Degree | Firstname | Lastname | Room | Phone | |
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B.Sc. | Maximilian | Block | – | – | |
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Asha | Knipp | – | – | ||
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B.Sc. | Pawel | Korzeb | – | – | |
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B.Sc. | Mira Tanja | Mahlein | – | – | |
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Lena | Mühlschlegel | – | – | ||
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B.Sc. | Yasmin | Saremi Nanji | – | – | |
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Luis Jakob | Walter | – | – | ||
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Ziyi | Wang | – | – |
Other Staff
| Photo | Degree | Firstname | Lastname | Room | Phone | |
|---|---|---|---|---|---|---|
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Dr. | Jonathan | Coles | EG.048 | – | |
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Susmita | De | – | – | ||
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M.Sc. | Christina | Frost | – | – | |
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Margrethe | Gaardlos | – | – | ||
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Ameya | Harmalkar | – | – | ||
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M.Sc. | Julian | Hartmann | 2701 | – | |
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Dr. | Korbinian | Liebl | – | +49 89 289-13697 | |
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Anshuman J. | Mahapatra | – | – | ||
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M.Sc. | Danial | Pour Jafar Dehkordi | 2059 | – | |
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B.Sc. | Arrien Symon | Rauh | – | – | |
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Jose | Roldan | – | – | ||
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Prof. Dr. | Philipp | Scherer | 2073 | – | |
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Neelanjana | Sengupta | – | – | ||
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Till | Siebenmorgen | 2059 | – | ||
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M.Sc. | Carlos Christian | Sustay Martinez | – | – |
Teaching
Course with Participations of Group Members
| Titel und Modulzuordnung | |||
|---|---|---|---|
| Art | SWS | Dozent(en) | Termine |
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Continuum Mechanics
eLearning-Kurs Zuordnung zu Modulen: |
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| VO | 4 | Zacharias, M. |
Mo, 14:00–16:00, PH HS2 Di, 08:00–10:00, PH HS2 |
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Quantum Mechanics of Molecular Systems
eLearning-Kurs LV-Unterlagen Zuordnung zu Modulen: |
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| VO | 2 | Scherer, P. |
Do, 10:00–12:00, PH 2271 |
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Exercise to Continuum Mechanics
eLearning-Kurs Zuordnung zu Modulen: |
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| UE | 2 |
Leitung/Koordination: Zacharias, M. |
Termine in Gruppen |
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Exercise to Quantum Mechanics of Molecular Systems
Zuordnung zu Modulen: |
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| UE | 2 | Scherer, P. | Termine in Gruppen |
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Praktikum Biophysik für Studenten der Biochemie eLearning-Kurs Zuordnung zu Modulen: |
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| PR | 4 | Bausch, A. Dietz, H. Lieleg, O. Rief, M. Simmel, F. … (insgesamt 7) | |
Offers for Theses in the Group
- Free energy calculation of protein-ligand binding
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Mit Hilfe von Moleküldynamiksimulationen sollen freie Energien der Bindung von einem Liganden an ein Enzymmolekül berechnet werden. Der Ligand hemmt die Aktivität des Enzyms durch Bindung an die aktive Tasche des Enzyms. Durch Simulationsstudien kann der Einfluss einzelner chemischer Gruppen auf die Bindeaffinität (=Stärke der Bindung) des Liganden untersucht werden. Ziel der Simulationsstudien ist es, die Bedeutung einzelner chemischer Gruppen für die Bindeaffinität zu analysieren und mögliche Wege zu Erhöhung der Affinität aufzuzeigen.
- suitable as
- Bachelor’s Thesis Physics
- Supervisor: Martin Zacharias
- Refinement of protein-peptide complexes using replica exchange with repulsive scaling
- The protein-peptide binding plays a major role for many cellular processes. The prediction how peptides interact with partner proteins is still an unsolved problem. In this BSc thesis a new method for improved sampling in Molecular Dynamics simulations will be used and tested on predicting the structure of protein-peptide complexes. The thesis gives important insights into molecular interactions but also in computer simulation methododologies.
- suitable as
- Bachelor’s Thesis Physics
- Supervisor: Martin Zacharias
Current and Finished Theses in the Group
- Implementation of Structure Based Models to Comprehend Protein Assembly Processes
- Abschlussarbeit im Masterstudiengang Physik (Biophysik)
- Themensteller(in): Martin Zacharias