The focus of research of the Regensburg group is NMR-structure determination of proteins, with the focus of high pressure NMR spectroscopy, general biochemistry, and software development for automated analysis of protein NMR data and protein structure prediction. NMR (and crystal) structures of a number of polypeptides and proteins have been solved in our group. The first program for the automated evaluation of two-dimensional NMR data of polypeptides was published by us 1984 (Neidig, Bodenmueller and Kalbitzer, Biochem. Biophys. Res. Comm. 125, 1143-1150). In the following years the program AURELIA was written in close cooperation with K.-P. Neidig (then at Bruker, Karlsruhe) which is devised for the general visualization, processing and evaluation of multidimensional NMRspectra of biomolecules (Neidig et al., 1995, J. Biomol. NMR. 6, 255-270). A first version of new program package AUREMOL (as independent part of AURELIA) has been written as a cooperation between the Regensburg group and the Bruker company. The AUREMOL-project is aimed to the completely automated structure determination of proteins from NMR data with a new top-down strategy. A first version of the program has been distributed (www.auremol.de) which contains new tools for the data display and evaluation, spectra simulation and structure validation. The program module KNOWNOE is used for the automated assignment of NOESY spectra using a novel knowledge based approach, the module RELAX-JT2 performs a complete simulation of NOESY-type spectra on the basis of the relaxation matrix formalism and includes detailed modeling of internal motions, J-coupling effects and transverse relaxation times. A new algorithm molecule centered approach (MCA) has been devised which automatically determines the 3D-structure of small proteins from a set of suitable nD-NMR spectra using an HMM-TA algorithm.

Recent relevant publications on software development.:

1. Schulte, A. C., Goerler, A., Antz, C., Neidig, K.-P. & Kalbitzer, H. R. (1997) Use of Global Symmetries in Automated Signal Class Recognition by a Bayesian Method. J. Magn. Reson. 129, 165-172.

2. Goerler, A., Gronwald, W., Neidig, K.-P. & Kalbitzer, H. R. (1999) Computer Assisted Assignment of 13C or 15N edited 3D-NOESY-HSQC Spectra Using Back Calculated and Experimental Spectra. J. Magn. Reson. 137, 39-45.

3. Gronwald, W., Kirchhoefer, R. Goerler, A., Kremer, W., Ganslmeier, B., Neidig, K.-P. & Kalbitzer, H. R. (2000) RFAC, a programm for automated NMR-R-factor estimation. J. Biomol. NMR 17, 137-151.

4. Gronwald, W., Moussa, S., Elsner, R., Jung, A., Ganslmeier, B., Trenner, J., Kremer, W., Neidig, K.-P., & Kalbitzer, H.R. (2002) Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J. Biomol. NMR 23, 271-287.

5. Gronwald, W. and Kalbitzer, H.R. (2004) Automated Structure Determination of Proteins by NMR Spectroscopy, Progr. NMR spectr. 44, 33-96.

6. Brunner, K., Gronwald, W., Trenner, J. M., Neidig, K.-P. & Kalbitzer, H. R. (2006) A General Method for the Unbiased Improvement of Solution NMR Structures by the Use of Related X-Ray Data, the AUREMOL-ISIC Algorithm. BMC Struct. Biol. 346, 301-305.

107. Boehm, M., Stadlthanner, K., Gruber, P., Theis, F. J., Lang, E. W., Tome, A. M., Teixeira, A. R., Gronwald, W. & Kalbitzer, H. R. (2006) On the use of simulated annealing to automatically assign decorrelated components in second-order blind source separation. IEEE Transact. Biomed.  Engineer. 53, 810-820.

7. Stadlthanner, K., Tome, A. M., Theis, F. J., Lang, E. W., Gronwald, W. & Kalbitzer, H. R. (2006) Separation of water artefacts in 2D NOESY protein spectra using congruent matrix pencils. Neurocomp. 96, 497-522.

8. Gronwald, W., Brunner, K., Kirchhoefer, R., Trenner, J., Neidig, K.-P. & Kalbitzer, H. R. (2007) AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein structures. J. Biomol. NMR 37, 15-30.

Workpackages

Partner 6 is coordinator of workpackage 4, and contributes to workpackages 1 and 2 as well as 3 and 5.