NMR Back-calculation Refinement

This section describes how to back-calculate NOESY spectra from a three-dimensional structure of a molecule, and how to refine an initial model by directly minimizing the difference between the observed 2D NOE intensities and those calculated by the full relaxation matrix approach. Spin diffusion effects are thus accounted for fully during the refinement. Derivatives with respect to atomic coordinates are calculated analytically (Yip and Case, 1989). An example of a refinement with this method is Nilges et al. (1991).

For further reading, see (Ernst, Bodenhausen, Wokaun, 1987), James et al. (1991), Keepers and James (1984), Lipari and Szabo (1982), Macura and Ernst (1980), Nilges et al. (1991), Solomon (1955), and Yip and Case (1989).

- Setup of the Relaxation Refinement

- The Relaxation Matrix
- Analytical Expression for the Gradient
- The Energy Term
- Cutoffs
- Assessing the Quality of the Final Structure
- Input of the Experimental Data
- Prediction of a NOESY Spectrum
- Refinement against NOESY Intensities
- Simultaneous Refinement with HO and DO Spectra
- Calculation of Different Values
- Grid Search for Optimal Correlation Time