Hierarchic inertial projection: A fast distance matrix embedding algorithm

We have designed an improved method for solving the embedding problem, which consists in generating molecular conformations satisfying prescribed distance restraints. The problem was broken up into smaller subproblems by carrying out separate embeddings of subsets of the original point set. The relative orientation of the subsets were then determined by an additional embedding and the final coordinates of the full point set were obtained by rigid-body translations and rotations. The new approach was found to be considerably faster than the traditional method, and produced high-quality results when built into DRAGON, a Distance Geometry-based protein modelling tool developed in our laboratory. The method has a number of promising applications including the fast generation of model conformations from a set of distance restraints and macromolecular docking simulations. Copyright (C) 1996 Elsevier Science Ltd