Related publications

Computer-aided assignment

  • Antz, C., Neidig, K.-P. & Kalbitzer, H. R. (1995)
    A General Bayesian Method for an Automated Signal Class Recognition in 2D NMR Spectra Combined with a Multivariate Discriminant Analysis. J. Biomol. NMR. 5, 287-296.

  • Baskaran, K., Kirchhöfer, R., Huber, F., Trenner, J., Brunner, K., Gronwald, W., Neidig, K.-P. and Kalbitzer, H. R. (2009)
    Chemical Shift Optimization in Multidimensional NMR Spectra by AUREMOL-SHIFTOPT. J. Biomol. NMR 43, 197-210.

  • Glaser, S. & Kalbitzer, H. R. (1987)
    Automated Recognition and Assessment of Cross Peaks in Two-Dimensional NMR Spectra of Macromolecules. J. Magn. Reson. 74, 450-463.

  • 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.

  • Groß, K.-H. & Kalbitzer, H. R. (1988)
    Distribution of Chemical Shifts in 1H Nuclear Magnetic Resonance Spectra of Proteins. J. Magn. Reson. 76, 87-99.

  • Kalbitzer, H. R., Neidig, K.-P., Geyer, M., Saffrich, R. & Lorenz, M. (1991)
    Pattern Recognition in Two-Dimensional NMR Spectra of Proteins. In 'Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance´ (J.C. Hoch, ed.) pp 175-190, Plenum Press, New York.

  • Kalbitzer, H.R. (1994)
    Computer- Aided Analysis of Multidimensional NMR Spectra. In "Two-dimensional NMR-Spectroscopy: Applications for Chemists and Biochemists" (W.R.Croasmun und R.Carlson, eds) pp 581-618, Verlag Chemie, Weinheim.

  • Neidig, P., Bodenmüller, H. & Kalbitzer, H. R. (1984)
    Computer Aided Evaluation of Two-Dimensional NMR Spectra of Proteins. Biochem. Biophys. Res. Comm. 125, 1143-1150.

  • Neidig, K.-P., Saffrich, R., Lorenz, M. & Kalbitzer, H. R. (1990)
    Cluster Analysis and Multiplet Pattern Recognition in Two-Dimensional NMR spectra. J. Magn. Reson. 89, 543-552.

  • Neidig, K.-P., Geyer, M., Görler, A., Antz, C., Saffrich, R., Beneicke, W., & Kalbitzer, H. R. (1995)
    AURELIA, a Program for Computer-Aided Analysis of Multidimensional NMR Spectra. J. Biomol. NMR. 6, 255-270.

  • Schulte, A. C., Görler, 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.

Processing

  • Böhm, M., Stadlthanner, K., Gruber, P., Theis, F. J., Lang, E. W., Tomé, 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.

  • Beneicke, W. & Kalbitzer, H. R. (1994)
    Data Filling in Two-Dimensional NMR Spectroscopy. J. Magn. Reson. A107, 134-140.

  • Geyer, M., Neidig, K.-P. & Kalbitzer, H. R. (1995)
    Automated Peak Integration in Multidimensional NMR Spectra by an Optimized Iterative Segmentation Procedure. J.Magn.Reson.B 109, 31-38.

  • Glaser, S. & Kalbitzer, H. R. (1986)
    Improvement of 2D NMR Spectra by Mean t1 Ridge Subtraction and Antidiagonal Reduction. J. Magn. Reson. 68, 350-354.

  • Maurer, T., & Kalbitzer, H. R. (1996)
    Indirect Referencing of 31P and 19F NMR Spectra. J. Magn. Reson. B 113, 177-178.

  • Malloni, W. M., De Sanctis, S., Tomé, A. M., Lang, E. W., Munte, C. E., Neidig, K. P. Kalbitzer, H. R. (2010)
    Automated solvent artifact removal and base plane correction of multidimensional NMR protein spectra by AUREMOL-SSA. J. Biomol. NMR 47, 101-111.

  • Mitschang, L., Neidig, K.-P. & Kalbitzer, H. R. (1990)
    Suppression of Oscillatory Artifacts in Two-Dimensional NMR spectra. J. Magn. Reson. 90, 359-362.

  • Neidig, K.-P. & Kalbitzer, H. R. (1988)
    Improvement of 2D NMR Spectra by Matching Symmetry-Related Spectral Features. Magn. Reson. Chem. 26, 848-851.

  • Neidig, K.-P. & Kalbitzer, H. R. (1990)
    Improved Representation of 2D NMR Spectra by Local Rescaling. J. Magn. Reson. 88, 155-160.

  • Neidig, K.-P. & Kalbitzer, H. R. (1991)
    Enhancement of Global Symmetries in Two-Dimensional NMR Spectra. J. Magn. Reson. 91, 155-164.

  • Saffrich, R. , Beneicke, W., Neidig, K.-P. & Kalbitzer, H. R. (1993)
    Baseline Correction in n-Dimensional NMR Spectra by Sectionally Linear Interpolation. J. Magn. Reson. B 101, 304-308.

  • Stadlhanner, K., Theis, F. J., Lang, E. W., Gronwald, W., Kalbitzer, H. R. (2003)
    A matrix pencil approach to the blind source separation of artifacts in 2D NMR spectra. Neur. Inform. Process. 1, 103-110.

  • Stadlthanner, K., Tomé, 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.

  • De Sanctis, S., Malloni, W. M., Kremer, W., Tomé, A. M., Lang, E. W., Neidig, K. P. Kalbitzer, H. R. (2011)
    Singular Spectrum Analysis for an Automated Solvent Artifact Removal and Baseline Correction of 1D NMR Spectra. J. Magn. Reson.210, 177-183.

  • De Sanctis, S., Malloni, W. M., Kremer, W., Lang, E. W., Kalbitzer, H. R. (2012)
    Independent component analysis (ICA) and singular spectrum analysis (SSA) for solvent artifact suppression in one-dimensional NMR spectroscopy: a comparative analysis. Trends Appl. Spectr. 9, 1-15.

Protein-ligand and protein-protein interaction

  • Schumann, F. H., Riepl, H., Maurer, T., Gronwald, W., Neidig, K.-P., & Kalbitzer, H. R. (2007)
    Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions. J. Biomol. NMR 39, 275-289.

Quality control

  • Baskaran, K., Brunner, K., Munte, C. E., Kalbitzer, H. R. (2010)
    Mapping of protein structural ensembles by chemical shifts. J. Biomol. NMR 48, 71-83.

  • Gronwald, W., Kirchhöfer, R. Görler, 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.

  • Gronwald, W., Brunner, K., Kirchhöfer, 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.

Simulations

  • Görler, A. & Kalbitzer, H. R. (1997)
    RELAX: A Flexible Program for the Analysis of NOESY-Spectra by Backcalculation Based on the Complete Relaxation Matrix Formalism. J. Magn. Reson. 124, 177-188.

  • Görler, 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.

  • Harsch, T., Dasch, C., Donaubauer, H., Baskaran, K., Kremer, W., Kalbitzer, H. R. (2013)
    Stereospecific Assignment of the Asparagine and Glutamine Side Chain Amide Protons in Random-Coil Peptides by Combination of Molecular Dynamic Simulations with Relaxation Matrix Calculations. Appl. Magn. Reson.44, 319-331.

  • Möglich, A., Weinfurtner, D., Maurer, T., Gronwald, W. & Kalbitzer, H. R. (2005)
    A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles. BMC Bioinform. 6:91.

  • Möglich, A., Weinfurtner, D., Gronwald, W., Maurer, T. & Kalbitzer, H. R. (2005)
    PERMOL: Restraint-based protein homology modeling using DYANA or CNS. Bioinform.21, 2110-2111.

  • Ried, A., Gronwald, W., Trenner, J. M., Brunner, K., Neidig, K.-P. & Kalbitzer, H. R. (2004)
    Improved simulation of NOESY spectra by RELAX-JT2 including effects of J-coupling, transverse relaxation, and chemical shift anisotropy. J. Biomol. NMR 30, 121-131.

Structure determination

  • 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.

  • Cano, C., Brunner, K., Baskaran, K., Elsner, R., Munte, C. E. and Kalbitzer, H. R. (2009)
    Protein structure calculation with data imputation: the use of substitute restraints. J. Biomol. NMR 45, 397-411.

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

  • Gronwald, W., Brunner, K., Kirchhöfer, R., Nasser, A., Trenner, J., Ganslmeier, B., Riepl, H., Ried, A., Schreiber, J., Elsner, R., Kalbitzer, H. R. & Neidig, K.-P. (2004)
    The new AUREMOL program. Automation of protein structure elucidation. Bruker Report 154/155, 11-14.

  • Gronwald, W. and Kalbitzer, H. R. (2010)
    Automated protein NMR structure determination in solution.In "Computational Biology" (D. Fenyo, ed) Humana Press, Chapter 7, 95-127.

 

 


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