Acta Phys. -Chim. Sin. ›› 2006, Vol. 22 ›› Issue (05): 622-626.doi: 10.1016/S1872-1508(06)60023-5

• ARTICLE • Previous Articles     Next Articles

Scoring Function for the Other-type Protein Complexes

SHEN Long-Zhu;LI Chun-Hua MA Xiao-Hui;CHANG Shan;CHEN Wei-Zu;WANG Cun-Xin;   

  1. College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, P. R. China
  • Received:2005-11-17 Revised:2006-02-16 Published:2006-04-28
  • Contact: WANG, Cun-Xin

Abstract: Based on the conclusion that different complexes have distinctive chemo-physical characters at interfaces,a specific scoring function was designed to select the effective structures in protein-protein docking procedure for the Other-type protein complexes, which are hard to predict. This scoring function was composed of the atomic contact energy (EACE), van der Waals, and electrostatic interaction energies. The weight of each term was obtained by the multiple linear regression approach. The test result on 17 Other-type complexes from CAPRI benchmark1 demonstrated that the combinatorial scoring function could delineate the interaction feature of the Other-type complexes and reflect the energy change during the complex formation, and it has certain capacity of discriminating effective structures fromnumbers of the docked modes. Compared to the residue pair potential (RP), the combinatorial score could gain a higher success rate. Ranking the predicted models of two targets in CARPI round 8, the combinatorial score also exhibits greater potential to distinguish the effective association modes.

Key words: Scoring function, Atomic contact energy, Residue pair potential, Other-type complexes, CAPRI