Ensemble Based Binding Energy Calculation Method.

<p>Our method is composed of three steps: structure sampling, energy matrix generation, and binding energy calculation. Initial complex structures were generated by superimposing the peptides of crystal structures to the modeled SH3 domains. For each initial complex the near binding state conformations were sampled by molecular dynamics simulation. Sampled structures were used in calculating the contribution of each amino acid on the binding energy on each position, which is converted into energy matrices. The resulting energy matrices were used to calculate the binding energy of peptides.