A simple Calpha-SC potential with higher accuracy for protein fold recognition

Biochem Biophys Res Commun. 2009 Feb 6;379(2):610-5. doi: 10.1016/j.bbrc.2008.12.131. Epub 2009 Jan 1.


In this paper, an improved C(alpha)-SC energy potential designed for protein fold recognition was reported. It consists of three extremely simple interaction terms which are supposed to be the dominant interactions in protein folding: residue-residue contact, hydrophobicity and pseudodihedral potentials. The potential function only contains 210 contacts, one hydrophobic and one torsion parameters, which have been optimized using an interior point algorithm of linear programming. Tests of the derived potential function on commonly used decoy sets illustrate that it outperforms most of the existing coarse-grained potentials in terms of its capabilities in recognizing native structures and consistency in achieving high Z-scores across decoy sets, and it has almost equivalent performance to the potentials which considered complex intra-molecular interactions. The results show that our scoring function is a generally prospective potential for protein structure prediction and modeling with regard to its recognition and computation efficacy.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbon / chemistry*
  • Models, Molecular*
  • Protein Conformation*
  • Protein Folding*
  • Proteins / chemistry*


  • Proteins
  • Carbon