Computational Biochemistry Group

Molecular modeling and simulation of biological macromolecules.


Head:  Dr. Stefan Fischer

University of Heidelberg
IWR, Im Neuenheimer Feld 368, room  222
D-69120 Heidelberg

Secr.: +49 (6221) 54-8858
Fax.:  +49 (6221) 54-8868


Group funding

Stefan Fischer obtained his Ph.D. in biophysics from Harvard University in 1992, in the theoretical chemistry group of Martin Karplus (2013 Nobel laureate), where he pioneered the development of computational methods for studying complex motions and reactions in proteins.  Since 1999, he heads the Computational Biochemistry group at the Interdisciplinary Center for Scientific Computing (IWR) of the University of Heidelberg.

Research interests

Proteins are the little "machines" that perform all the tasks in living systems. To understand in a quantitative way how they function at the atomic level of detail, it is necessary to use computer simulations, because there are no experimental techniques that would allow to observe all the atoms of a protein on the ultra-fast time-scale of their motion (which is on the order of 10-14 seconds). Our main research focus has been on protein nanomachines, such as molecular motors, trans-membrane pumps and channels and catalytic enzymes.

Aside from using the now standard Molecular Dynamics methods, we develop algorithms for finding reaction paths and transition states in high-dimensional systems. This enables us to study complex biomolecular processes that occur on time-scales beyond the scope of standard molecular dynamics (i.e., slower than micro-seconds), such as the motions of molecular motors in muscle. We also use combined quantum/classical mechanics (QM/MM), which allow to accurately study chemical reactions inside proteins, such as occurring in enzymatic catalysis.

For all these different systems, we closely collaborate with experimental research groups.  The resulting knowledge serves to optimize processes in biochemical engineering, to inspire developments in the nanotechnologies, and to help pharma and biotechnological research.

Research projects:


Former/Present Students


Masters/PhD/Postdoc positions