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 geometric contact measure and the 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. [NLWN94] and Fisc...