Theoretical and Computational Biophysics Group
Beckman Institute, Room 3061
University of Illinois at Urbana-Champaign
405 N. Mathews Ave.
Urbana, IL 61801, USA.
- Oct 2002-Nov 2007 PhD, Institute of Biochemistry, Charite - Universitätsmedizin Berlin, Germany
- May 2001-April 2002 visiting scholar at the Theoretical and Computational Biophysics Group
- 1998-2001 studied biophysics (Hauptstudium) at Humboldt University Berlin, Germany.
- 1996-1998 studied biology (Grundstudium) at University of Konstanz, Germany.
I'm developing scientific tools for VMD.
I also wrote the
SymmetryTool plugin which provides an easy-to-use graphical
interface to the "measure symmetry" command (for which I also developed the
algorithm). It determines the symmetry pointgroup of a given selection and
displays the symmetry elements. The underlying algorithm is very robust and
can handle molecules whose coordinates deviate to a certain extent (controlled
by a tolerance parameter) from the ideal symmetry. The closest match with the
highest symmetry is returned. Atoms can be snapped into idealized symmetric
Further I'm working on the improvement of the
Implicit Ligand Sampling (ILS) method.
We achieved significant speedups of ILS up by improving the CPU version of the code
and by adding parallel versions that use SSE, multiple CPUs or GPUs.
Further, I provided a
graphical user interface for setting up ILS calculations.
Another goal is to extend the GUI to suport analysis and visualization of ILS results.
One of my main scientific interests are oxygen migration pathways in proteins. The following project was done while I was working at the Charite in Berlin:
Identification of Dynamic Oxygen Access Pathways in 12/15-LipoxygenaseCells contain numerous enzymes utilizing molecular oxygen for their reactions. Often, their active sites are buried deeply inside the protein which raises the question whether there are specific access channels guiding oxygen to the site of catalysis. Choosing 12/15-lipoxygenase as a typical example for such oxygen dependent enzymes we determined the oxygen distribution within the protein and defined potential routes for oxygen access. For this purpose we have applied an integrated strategy of structural modeling, molecular dynamics simulations, site directed mutagenesis and kinetic measurements.
Distribution of oxygen in lipoxygenase shown in terms of free energy isosurfaces
(yellow). Red arrows indicate the energetically most favorable oxygen access route
connecting a high affinity region at the protein surface with the catalytic center.
Above, the energy profile along this path is projected. The
grey line marks the level of the drawn energy isosurface.
General scientific interests:
Stone JE, Saam J, Hardy DJ, Vandivort KL, Hwu WW, and Schulten K.
Saam J, Ivanov I, Walther M, Holzhütter H, and Kuhn H. (2007)
Ivanov I, Saam J, Kühn H, Holzhütter H. (2005)
Kühn, H, Saam J, Eibach S, Holzhütter H, Ivanov I, Walther M. (2005)
Ernsting NP, Kovalenko SA, Senyushkina T, Saam J and Farztdinov V. (2001)