Introduction

CSS-0 is a web server that calculates binding energy of a protein-protein interaction using the protein complex structure. Here a simple mean-field approach is employed to achieve accuracy and speed simultaneously.

The mean-field scoring function is generated by the PPI.CSS scheme, which optimizes a scoring function with respect to a given dataset by iteratively adding and removing energy term candidates. In CSS-0, we compiled 22 energy term candidates consisting of a contact energy term represented by the μ-potential score, as well as accessible solvation area terms. Optimization with respect to a general protein binding energy benchmark leads to the final scoring function, composed of only 4 simple energy terms.

Despite its simplicity, the function turns out to be considerably reliable in predicting experimental binding energy of a protein complex. Also, CSS-0 shows its desirable performance in reproducing biologically relevant results when applied to a proteomic database.


For details of the method, please refer to the following paper:

Jeong-Mo Choi, Adrian W. R. Serohijos, Sean Murphy, Dennis Lucarelli, Leo L. Lofranco, Andrew Feldman, and Eugene I. Shakhnovich, "A Fast Predictor of Protein Binding Energy at a Proteomic Scale," Submitted 2013