• protein;
  • block;
  • energy function;
  • orientation;
  • cluster


Blocks are the selected portions of amino acids. They have been used effectively to represent amino acids in distinguishing the native conformation from the decoys. Although many statistical energy functions exist, most of them rely on the distances between two or more amino acids. In this study, the authors have developed a pairwise energy function “DOKB” that is both distance and orientation dependent, and it is based on the key blocks that bias the distal ends of side chains. The results suggest that both the distance and the orientation are needed to distinguish the fine details of the packing geometry. DOKB appears to perform well in recognizing native conformations when compared with six other energy functions. Highly packed clusters play important roles in stabilizing the structure. The investigation about the highly packed clusters at the residue level suggests that certain residue pairs in a low-energy region have lower probability to appear in the highly packed clusters than in the entire protein. The cluster energy term appears to significantly improve the recognition of the native conformations in ig_structal decoy set, in which more highly packed clusters are contained than in other decoy sets. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 681–692, 2014.