Distance geometry efficiency

Kuszewski, Nilges, M., Brunger, A. T. Sampling and efficiency of metric matrix distance geometry a novel partial metrization algorithm./. Biomol. NMR 1992, 2, 33 55. 

J. Kuszewski, M. Nilges, and A. T. Briinger, ]. Biomol. NMR, in press. Sampling and Efficiency of Metric Matrix Distance Geometry A Novel Partial Metrization Algorithm. 

Fig. 2. Schematic representation of conformational space exploration efficiencies and their dependency for the different sampling scale with, insufficient (A), nearly sufficient (B), and almost sufficient (C) number of initial structures. In this example, preliminary calculations are distance geometry or torsion angle space algorithms, and refinement is restraint molecular dynamics with same set of NMR-derived structural information. The exploration extents of the refinements are assumed to be similar for selected preliminary calculation s results (i.e., initial structures of the refinement calculations).

The ensemble distance geometry pharmacophore modeling approach of Sheridan et al. (145) provides the most direct and efficient method for... 

All possible conformers lie between these upper and lower distance bounds—the task of distance geometry is to convert or embed this usually uncertain distance information into accurate three-dimensional Cartesian coordinates. Crippen and HavePi solved the problem for the case of an exact distance matrix, where all distances are known. Much additional effort has gone into finding efficient and practical methods for solving the general problem of a distance bounds matrix, where only a subset of the distances is known exactly. This remains a very difficult problem for large molecules with more than 1000 atoms. 

Efficiency of Metric Matrix Distance Geometry—A Novel Partial Metrization Algorithm. 

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