Prediction of protein structural class with Rough Sets

Youfang Cao¹ , Shi Liu¹ , Lida Zhang¹ , Jie Qin¹ , Jiang Wang¹ and Kexuan Tang¹^,2

¹Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Institute of Systems Biology, Shanghai Jiao Tong University, Shanghai 200030, China

²State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, Morgan-Tan International Center for Life Sciences, Fudan University, Shanghai 200433, China

author email corresponding author email

BMC Bioinformatics 2006, 7:20doi:10.1186/1471-2105-7-20


Published:	14 January 2006

Abstract

Background

A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the decision system, decision rules are generated, which can be used to classify new objects.

Results

In this study, self-consistency and jackknife tests on the datasets constructed by G.P. Zhou (Journal of Protein Chemistry, 1998, 17: 729–738) are used to verify the performance of this method, and are compared with some of prior works. The results showed that the rough sets approach is very promising and may play a complementary role to the existing powerful approaches, such as the component-coupled, neural network, SVM, and LogitBoost approaches.

Conclusion

The results with high success rates indicate that the rough sets approach as proposed in this paper might hold a high potential to become a useful tool in bioinformatics.