Recent:

CMView
Decomposition of Protein structures and Visualisation in 2D/3D

Reconstruct
An example of implementing a basic reconstruction pipeline using TINKER

My Own Histone
Build your own Histone/Nucleosome model (in German)

OWL
Java toolkit for computational structural biology with special emphasis on graph analysis of protein structures

Residue interaction graph in MHC1 (Visualization with Pymol)

In this context, moving on to higher level definitions of protein function, the question of how complex networks can be decomposed into meaningful subsets arises. In order to formulate experimentally verifiable hypotheses the functional maps must be made accessible to human interpretation. I have developed a method that reliably extracts whole signal-transduction pathways. Here complex sets of protein associations derived from text-mining the biological literature are used as an example of the complex and noisy environment information is processed within the cell.

By building a concise model of the overall information gain in the field of proteomics I formulated an algorithmic strategy that enables the proteomics community to build a reliable scaffold of the interactome in a fraction of the time compared to un-coordinated efforts. This work opens the door to a new breed of methods and strategies which actively use the scale-free properties of biological networks to their advantage. Potential applications of this strategy to structure prediction and docking are currently investigated. As a result, the resulting methods are able to approximate NP-hard problems in bioinformatics effectively by relatively simple computational means.

We want to develop novel and improved experimental and computational high-throughput methods for the detection of physiological relevant interactions. The integration of experimental results with in-silico analysis and predictions in an interactive cycle should prove mutually beneficial on the path towards elucidating the (human) interactome.