A simple Cα-SC potential with higher accuracy for protein fold recognition
In this paper, an improved Cα-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 intramolecular 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.
Junfeng Gu Honglin Li Hualiang Jiang Xicheng Wang
State Key Laboratory of Structural Analysts for Industrial Equipment, Department of Engineering Mech Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Mater
国际会议
武汉
英文
677-682
2010-09-01（万方平台首次上网日期，不代表论文的发表时间）