Evaluation of several prediction methods of membrane protein structure and topology

Qi Liu, Zhongqiang Chen, Yixue Li, Baohua Wang and and Yisheng Zhu

1. Bioinformation Center, Shanghai Institutes for Biological Sciences,
Chinese Academy of Sciences
2. Department of biomedical engineering,
Shanghai Jiaotong University

ABSTRACT

Since present prediction methods of membrane protein structure and topology made use of mixed data sets both from experiments and prediction as training and test sets, the reliability and accuracy of their prediction is still under debate. To benchmark the performance of these methods, this paper uses a test set of membrane proteins created by EBI with either available 3-D structure or experimentally confirmed transmembrane regions. Then the prediction results are compared and the problems existing in these methods and important features for successful prediction are pointed out. Based upon recent advances in membrane protein, possible means to improve topology prediction accuracy are discussed.