The embedding problem for predistance matrices

Abstract

A fundamental problem in molecular biology is the determination of the conformation of macromolecules from NMR data. Several successful distance geometry programs have been developed for this purpose, for example DISGEO. A particularly difficult facet of these programs is the embedding problem, that is the problem of determining those conformations whose distances between atoms are nearest those measured by the NMR techniques. The embedding problem is the distance geometry equivalent of the multiple minima problem, which arises in energy minimization approaches to conformation determination. We show that the distance geometry approach has some nice geometry not associated with other methods that allows one to prove detailed results with regard to the location of local minima. We exploit this geometry to develop some algorithms which are faster and find more minima than the algorithms presently used.