Sparse restraints, structural refinement

Free Energy Computational Studies Structure Refinement with Sparse Restraints... 

The well-known difficulties in calculating tliree-dimensional structures of macromolecules from NMR data mentioned above (sparseness of the data, imprecision of the restraints due to spin diffusion and internal dynamics) also make the validation of the structures a challenging task. The quality of the data [88] and the energy parameters used in the refinement [89] can be expected to influence the quality of structures. Several principles can be used to validate NMR structures. 

Konnert s technique for refining the structure of proteins subject to known geometrical constraints has been developed by incorporating restraints on the variances of the interatomic distributions, in order to express the retention of local geometry that accompanies certain modes of motion." As as alternative to the sparse matrix approach, Hoad and Norman have utilized the fast Gauss-Seidel least-squares routine for the refinement of atomic co-ordinates." A comparison has been made of the structures obtained for bovine trypsin (EC 3.4.24.4) by the difference Fourier and real space refinement methods." ... 

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