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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.