We present an energy function for predicting binding free energies of protein-protein complexes, using the 3-dimensional structures of the complex and unbound proteins as input. Our function is a linear combination of 9 terms and achieves a correlation coefficient of 0.63 with experimental measurements when tested on a benchmark of 144 complexes using leave-one-out cross validation. Although we systematically tested both atomic and residue-based scoring functions, the selected function is dominated by residue-based terms. Our function is stable for subsets of the benchmark stratified by experimental pH and extent of conformational change upon complex formation, with correlation coefficients ranging from 0.61 to 0.66. We compare our function with a variety of other functions. Our function shows the best overall performance. Only for antibody-antigen complexes some other functions perform better, which is due to the bias towards residue-based terms in our function. [Protein Science vol. 21, p. 396-404, 2012]

Prediction of protein-protein binding free energies

244th National Meeting (2012)

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