Pattern recognition strategies for molecular surfaces. II. Surface complementarity.
Fuzzy logic based algorithms for the quantitative treatment of complementarity of molecular surfaces are presented. Therein, the overlapping surface patches defined in article I1 of this series are used. The identification of complementary surface patches can be considered as a first step for the solution of molecular docking problems. Standard technologies can then be used for further optimization of the resulting complex structures. The algorithms are applied to 33 biomolecular complexes. After the optimization with a downhill simplex method, for all these complexes one structure was found, which is in very good agreement with the experimental results.
Exner
Thomas E
TE
Department of Chemistry, Mathematical Chemistry Research Unit, University of Saskatchewan, 110 Science Place, Saskatoon, SK, Canada, S7N 5C9.
Keil
Matthias
M
Brickmann
Jürgen
J