Abstract—Amino acid-nucleotide base pair potentials are used to screen docked complexes generated by DOT. The pair potential algorithm designed in this paper is applied to screening 10 systems selected from protein-DNA benchmark set. For all the systems, a correct docking was placed within the top 6% of the pair potential score ranked complexes. Also, over 60% correct answers rank in the top 10% of the docked results for most of the systems.

Index Terms—Amino acid-nucleotide base pair potentials, protein-DNA dock, screening.

The authors are with College of Informatics, South China Agricultural University, 510642, Guangzhou, China (email address: ldmfs@126.com, schang@scau.edu.cn, c-j1987@163.com, tianxuhong@scau.edu.cn).

 

Cite:Dongmin Liu, Shan Chang, Jian Chen, and Xuhong Tian, "Use of Amino Acid-Nucleotide Base Pair Potentials in Screening Protein-DNA Docked Complexes," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 3, no. 5, pp. 420-423, 2013.