Empirical Parameters for Estimating Protein-Protein Binding Energies:Number of Short- and Long-Distance Atom-Atom Contacts

The number of atom-atom contacts in long distance can fit to the experimental binding energies in a dataset containing 151 experimental data with the correlation coefficient about 0.68. Based on this factor, a set of distancedependent empirical potentials for various types of short-distance (2.4 Å-5 Å) contacts was obtained by guided fitting, i.e. a set of two parameters fitting. Incorporation of these short-distance potentials improved the correlation coefficients to 0.881.