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Abstract:
We have developed and
implemented a parallel distributed algorithm for the
rigid-body protein docking problem. The algorithm is based on
a new fitness function for evaluating the surface matching
of a given conformation.
The fitness function is defined as the weighted sum
of two contact measures, the {\em geometric contact measure}
and the {\em chemical contact measure}.
The geometric contact measure measures the ``size'' of the
contact area of two molecules. It 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).
The chemical contact measure is also based
on the ``van der Waals contacts'' principle: We consider
all atom pairs that have a ``van der Waals'' contact,
but instead of adding a constant for each pair $(a,b)$ we add a
``chemical weight'' that depends on the atom pair $(a,b)$.
We tested our docking algorithm with a test set that contains
the test examples of Norel et al.~\cite{NLWN94} and
\protect{Fischer} et al.~\cite{FLWN95} and compared the results of our
docking algorithm with the results of Norel et al.~\cite{NLWN94,NLWN95},
with the results of Fischer et al.~\cite{FLWN95} and
with the results of Meyer et al.~\cite{MWS96}.
In 32 of 35 test examples the best conformation with respect
to the fitness function was an approximation of the real
conformation.
