A distance and orientation dependent potential energy function with cluster energy

Although there have been many potential energy functions to evaluate protein structures, it is still a major challenge to develop an effective energy function. Most potential energy functions do not distinguish a pair of interacting residues in the densely packed environment from the loosely packed environment. We have developed a block pair-specific function that is both distance and orientation dependent. Instead of using the entire side-chain to represent the residue, our function is built on one or two key blocks of each side chain. We show that the probability for seeing low-energy pairs in the highly packed clusters is not the same as that in the entire protein structure for certain pairs. We introduced a cluster energy term in the potential function to represent such difference. In a test of 5 decoy sets, our cluster-energy-adjusted function using key blocks (CEAKB) appears to perform comparably as OPUS-PSP in three decoy sets in spite of its reduced representation of the side chain blocks. CEAKB has better recognition of the native structures in the other two sets of decoys.