Calculation of binding energies using a robust molecular mechanics technique: application to an antibody-antigen...

A novel molecular mechanics technique, which is both computationally efficient and robust, for calculation of relative stability of macromolecules and binding energies is presented. The technique delivers exact results for a number of hypothetical systems; the technique can be used to energy minimize a number of similar macromolecules simultaneously; simultaneous minimization of many structures requires computer time only fractionally over that needed to energy minimize one such structure. The method has been used to successfully calculate the relative stability and binding of two avian lysozymes to the monoclonal antibody D1.3.