Former Sühnel Research Group (until 2011)

Biocomputing: Structural bioinformatics and computational genomics

Jürgen Sühnel has retired as FLI Group Leader in June 2011. He is still affiliated with the institute as coordinator of JenAge.

We did research in the field of bioinformatics and computational biology with an emphasis on structural biology and computational genomics. In the structural biology field we have been interested in the identification and analysis of unusual motifs and interactions in three-dimensional structures of proteins and nucleic acids. Our research involved different techniques including quantum-chemical calculations, molecular dynamics simulations and structural bioinformatics approaches.

More specifically, we have worked

  1. water-mediated interactions in nucleic acid base pairs,
  2. the geometry and electronic structure of base tetrad motifs occurring in telomere structures, for example,
  3. C-H...O-, C-H...N- and C-H...PI interactions,
  4. the role of non-repetitive dipeptide motifs in proteins that correspond to transitions between different Ramachandran plot clusters.
Telomeric DNA sequences form DNA tetraplex structures, see for example the structure of the human telomeric repeat sequence.
Sühnel: Telomeric DNA sequences
Quantum-chemical studies on building blocks such as the sandwiched G-tetrads shown above can contribute to a better understanding of structure and function.
Sühnel: Sandwiched G-tetrad

Last Projects & Collaborations

Our computational genomics work was aimed at the development of tools for an accelerated and improved annotation and analysis of prokaryotic genomes. In addition, a new genome browser type that encodes the nucleic acid sequence by physico-chemical dinucleotide properties was developed. We also applied mathematical methods to microscopical, FISH (fluorescence in situ hybridization) and imaging techniques.

We have developed and are maintaining a variety of widely used databases and webtools as e.g.:

Circular plot of features of the E. coli K12 genome generated with JPGV. CDS(PDB) stands for genes for which three-dimensional protein structures are available. Note, that the origin of replication correlates with the purine excess minimum (Romualdi et al, 2007).
Sühnel: Circular plot of features of the E. coli K12 genome

The Sühnel Group was coordinating the Jena Centre for Bioinformatics - JCB between 2001 and 2007. Currently, Jürgen Sühnel is acting as the coordinator of The Jena Centre for Systems Biology of Ageing - JenAge.

In-house collaborations:

With the Diekmann Lab and Platzer Lab.


External collaborations:

  • M. Meyer, Revotar Biopharmaceuticals, Hennigsdorf,
  • C. Skerka and P. Zipfel, Hans Knöll Institute, Jena,
  • A. Gutermann, Medigene, Martinsried,
  • P. Dittrich, Jena University,
  • M. Hausmann, Heidelberg University
  • E.B. Pedersen, University of Southern Denmark, Odense

Contact

Dr. Jürgen Sühnel

Jürgen Sühnel
Coordinator JenAge
+49 3641 65-6200
juergen.suehnel@leibniz-fli.de