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Abstract A very efficient algorithm for determining the geometrically feasible binding modes of a flexible ligand molecule at the receptor site is presented. It is based on distance geometry but maintains the requirements of three dimensions. The distance geometry manipulation can superimpose two bodies without explicitly calculating the necessary rigid rotation and translation. The whole conformation space of a flexible molecule can be efficiently examined by considering only a finite number of conformational points. The method is suitable only when the criterion for superposition is some minimum distance limit. It cannot, however, give the exact distance between two points in two different bodies.
Ghose et al. (Tue,) studied this question.