b'@techreport{Lenhof97,'b'\nTITLE = {New contact measures for the protein docking problem},\nAUTHOR = {Lenhof, Hans-Peter},\nLANGUAGE = {eng},\nNUMBER = {MPI-I-97-1-004},\nINSTITUTION = {Max-Planck-Institut f{\\"u}r Informatik},\nADDRESS = {Saarbr{\\"u}cken},\nYEAR = {1997},\nDATE = {1997},\nABSTRACT = {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.},\nTYPE = {Research Report},\n}\n'