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An algorithm for the protein docking problem


Lenhof,  Hans-Peter
Algorithms and Complexity, MPI for Informatics, Max Planck Society;

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Lenhof, H.-P.(1995). An algorithm for the protein docking problem (MPI-I-1995-1-023). Saarbrücken: Max-Planck-Institut für Informatik.

We have implemented a parallel distributed geometric docking algorithm that uses a new measure for the 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 $c_a$ 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 bound of the interval an integer constant $c_s$ is subtracted from the potential ($c_a <c_s$). 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. Among the best five dockings found by the algorithm there was almost always a good (rms) approximation of the real conformation. 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 {\it et al.}[NLW+]. The parallel version of the algorithm has a reasonable speedup and modest communication requirements.