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Abstract:
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.
