Computer Simulation of Protein-Protein and Protein-Peptide Interactions
Final rept. Jan 92-31 Mar 93,
STANFORD UNIV CA EDWARD L GINZTON LAB OF PHYSICS
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A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicity maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form. Further work has been done on predicting the affinity of various Avian lysozymes for a couple of antibodies.
- Numerical Mathematics