Neighbourhood preference based energy function and its applications in structure prediction and protein evolution

Based on the statistics from known structures in the protein data bank, a statistical energy function is derived to reflect the amino acid neighbourhood preferences. The neighbourhood of one amino acid is defined by its contacting residues, and the energy function is determined by the neighbhoring residue types and relative positions. A scoring function, Nepre, has been implemented and its performance was tested with several decoy sets. The results show that the Nepre program can be applied in model ranking to improve the success rate in structure predictions. We also applied this empirical energy function in the understanding of protein evolution and the designability of protein structures.