An Algorithm for the Protein Docking Problem

Abstract

We have implemented a parallel distributed geometric docking algorithm that uses a new measureforthe size of the contact area of two molecules. The measure is a potential function that counts the “van der Waals contacts” between the atoms of the two molecules ( the algorithm does not compute the Lennard-Jones potential). An integer constant c, is added to the potential for each pair of atoms whose distance is in a certain interval. For each pair whose distance is smaller than the lower boundofthe interval an integer constant c, is subtracted from the potential (cg < c,). The number of allowed overlapping atom pairs is handled by a third parameter N. Conformations where more than N atom pairs overlap are ignored. In our “real world” experiments we have used a small parameter N that allows small local penetration. The algorithm almost always found good (rms) approximations of the real conformations that were among the best five geometric dockings. In 42 of 52 test examples the best conformation with respect to the potential function was an approximation of the real conformation. The running time of our sequential algorithm is in the order of the running time of the algorithm of Norel et al. [NLW+]. Theparallel version of the algorithm has a reasonable speedup and modest communication requirements.