My research at the EMBL and the Pasteur Institute was focussed on structural bioinformatics and structural genomics comprising methods from sequence analysis, modelling and molecular dynamics. Structural bioinformatics is concerned with computational approaches to predict and analyse the spatial structure of proteins and nucleic acids and to derive their function in the cell. Structural genomics is the systematic effort to gain a complete structural description of a defined set of molecules, ultimately for an organism’s entire proteome. Structural genomics projects apply X-ray crystallography and NMR spectroscopy in a high-throughput manner.

In Michael Nilges' group, I was working on the ARIA software for automated NOE assignment to speed up structure determination from NMR data. The most important experimental parameter for the determination of biomolecular structures is the nuclear Overhauser effect (NOE). Although NOEs can only be measured between nuclei not farther apart than approximately 0.5 nm, they provide a wealth of interproton distances within and in between residues. Unfortunately, the interpretation of the NOE spectra is complicated by the high number of possible assignments, noise and heavy overlap. A substantial amount of time is therefore spent for interpretating and assigning NOE spectra. With increasingly bigger systems, a completely manual approach for the assignment of the NOEs is too cumbersome and time-consuming. Thus, automation of the NOE assignment and structure calculation process has become an important issue. ARIA leads to a substantial speed-up of structure calculation by automation of the NOE assignment process. Compared with a manual approach where initial structures are calculated based on a small fraction of the NOEs, the automated approach uses much more data to direct the calculation from the start.

ARIA comprises a relaxation matrix refinement algorithm that corrects the target distances for spin diffusion in each round of automated NOE assignment. Spin diffusion corrected target distances allow the choice of smaller error bounds. Eventually, this leads to a clearer distinction between signal and noise.

I was studying different non-bonded parameters of force fields for NMR structure calculation and their influence on the quality of the resulting NMR solution structures. The results clearly indicate that larger vdW radii than commonly employed in virtually all NMR structure calculation programs significantly improve the quality of the structures, if appropriate corrections for 1-4 interactions are employed. A hybrid PROLSQ/CSDX force field yields high quality structures.

A refinement of biomolecular structures in a thin layer of explicit solvent improves the quality of biomolecular structures. To illustrate the refinement procedure, please have a look at a trajectory of an HRDC domain in water as mpg movie (6.3 MB) calculated with a hybrid CSDX/OPLS force field.

The increased speed of structure determination necessary for the structural genomics projects make an independent validation of the structures particularly important, e.g., by comparison to expected properties. Structure validation helps to correct obvious errors and leads to a more standardized representation of structural data, e.g., by agreeing on a common atom name nomenclature. The knowledge of the structure quality is a prerequisite for further use of the structure in molecular modelling or drug design.

As part of an effort to improve data representation and data exchange, I was working on XML representation of NMR data. StarDOM is a software package to transform data provided in the Self Defining Text Archival and Retrieval (STAR) format into XML. This opens new possibilities for visual editing, archiving, parsing and structured queries of structural biology data. This work eventually lead to a collaboration with the CCPN project which aims to establish a common standard for NMR data, spectrum and structure files.

For further reading please have a look at the following publications:

• Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.
  M Fossi, J Linge, D Labudde, D Leitner, M Nilges, H Oschkinat
  Journal of Biomolecular NMR (2005) 31, 21-34.
  [PubMed] [pdf]
  
  
• Structural Bioinformatics and NMR structure determination.
  JP Linge and M Nilges
  Nucleic Acids and Molecular Biology Vol. 15 Practical Bioinformatics
  Springer-Verlag, Berlin, Heidelberg (2004), 123-137.
  [pdf]
  
  
• Correction of spin diffusion during iterative automated NOE assignment.
  JP Linge, M Habeck, W Rieping and M Nilges
  Journal of Magnetic Resonance (2004), 167, 334-342.
  [PubMed] [pdf]
  
  
• NOE assignment with ARIA 2.0: the nuts and bolts.
  M Habeck, W Rieping, JP Linge and M Nilges
  Methods in Molecular Biology (2004), 278, 379-402.
  [PubMed] [pdf]
  
  
• Refinement of protein structures in explicit solvent.
  JP Linge, MA Williams, CA Spronk, AM Bonvin and M Nilges
  Proteins Struct. Funct. Genet. (2003), 50, 496-506.
  [PubMed] [pdf]
  
  
• ARIA: automated NOE assignment and NMR structure calculation.
  JP Linge, M Habeck, W Rieping and M Nilges
  Bioinformatics (2003), 19, 315-316.
  [PubMed] [pdf]
  
  
• Bioinformatics - a definition.
  M Nilges and JP Linge
  Encyclopedic Reference of Molecular Pharmacology, ISBN: 3-540-428437,
  Springer-Verlag (2003)
  [html] [pdf]
  
  
• The CCPN project: an interim report on a data model for the NMR community.
  R Fogh, J Ionides, E Ulrich, W Boucher, W Vranken, JP Linge, M Habeck, W Rieping, TN Bhat, J Westbrook, K Henrick, G Gilliland, H Berman, J Thornton, M Nilges, J Markley and E Laue
  Nature Structural Biology (2002), 9, 416 - 418.
  [PubMed] [pdf]
  
  
• Improving the quality of protein structures derived by NMR spectroscopy.
  CA Spronk, JP Linge, CW Hilbers and GW Vuister
  Journal of Biomolecular NMR (2002), 22, 281-299.
  [PubMed] [pdf]
  
  
• Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression.
  K Zanier, I Luyten, C Crombie, B Muller, D Schumperli, JP Linge, M Nilges and M Sattler
  RNA (2002), 8, 29-46.
  [PubMed] [pdf] [pdb]
  
  
• Automated Assignment of Ambiguous Nuclear Overhauser Effects with ARIA.
  JP Linge, SI O'Donoghue and M Nilges
  Methods in Enzymology (2001), 339, 71-90.
  [PubMed] [pdf]
  
  
• New methods for automated NOE assignment and NMR structure calculation.
  JP Linge (2001)
  Book on Demand Verlag, Norderstedt, Germany.
  ISBN: 383111482X
  [amazon.de]
  
  
• New methods for automated NOE assignment and NMR structure calculation.
  JP Linge
  B.I.F. Futura (2001), 16, 206-209.
  [pdf]
  
  
• Refinement of the protein backbone angle psi in NMR structure calculations.
  R Sprangers, MJ Bottomley, JP Linge, J Schultz, M Nilges and M Sattler
  Journal of Biomolecular NMR (2000), 16 , 47-58.
  [PubMed] [pdf]
  
  
• The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins.
  Z Liu, MJ Macias, MJ Bottomley, G Stier, JP Linge, M Nilges, P Bork and M Sattler
  Structure (1999), 7, 1557-1566.
  [PubMed] [pdf] [pdb]
  
  
• StarDOM: from STAR format to XML.
  JP Linge, M Nilges and L Ehrlich
  Journal of Biomolecular NMR (1999), 15, 169 - 172.
  [PubMed] [pdf]
  
  
• Influence of non-bonded parameters on the quality of NMR structures: a new force-field for NMR structure determination.
  JP Linge and M Nilges
  Journal of Biomolecular NMR (1999), 13, 51 - 59.
  [PubMed] [pdf]



• Time-resolved UV/VIS-, FTIR- and ESR-spectroscopic investigation of the folding of Cytochrome c (Zeitaufgelöste UV/VIS-, FTIR- und ESR-spektroskopische Untersuchung der Faltung von Cytochrom c).
  JP Linge
  Diploma thesis, Ruhr-Universität Bochum (1997)
  [pdf]