Based on Dockground, We developed a low-resolution scoring funcion for protein-protein docking. Each residue is represented as one pseudo-atom, the "centroid" of the side chain. Using this scoring function, We attended CAPRI Scoring blind test. In this round, we tested on two protein-protein docking targets: Target 32 and Target 36. For Target 36, there is no near-native solution in decoy set. The result shows that our scoring function can successfully pick up two acceptable predictions: T32_S16.M05 and T32_S16.M03 (Target 32 Scoring Result). They are ranked in the third and fifth in our top 10 list.
If you feel it is useful, please cite:
Shiyong Liu, Ilya Vakser DECK: Distance-scale environment-dependent coarse-grained knowledge-based potentials for protein-protein docking (2011, BMC Bioinformatics)
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