Motif analysis and identification of antifreeze protein sequences
Antifreeze proteins (AFPs),which are also known as thermal hysteresis proteins,are ice-binding proteins.AFPs can adsorb to ice crystal surface and inhibit the growth of ice crystals in solution.But the interaction between AFPs and ice crystal is not known completely.Analyzing physicochemical characteristics of AFPs sequences is very significant to understand the ice-protein interaction.Through the analysis of the sequence motif by MEME,hydrophobic amino acids shown blue are most.According to the hydropathy,acid-base property,the chemical structure of the R group of amino acid and the polarity of the amino acids,the amino acids are respectively divided into 6 groups,3 groups,6 groups,4 groups.In this study,based on the n-Peptide compositions and these physicochemical characteristics,an algorithm of Support Vector Machine (SVM) is proposed for predicting antifreeze proteins.The best results of the jackknife test show that the sensitivity,the specificity,the overall identification accuracy and the Mcc value are 93.14%,96.08%,94.62% and 0.8927,respectively.The hydropathy and the chemical structure of the R group of amino acid are important physicochemical characteristics for identifying AFPs.
motif AFPs physicochemical characteristics SVM amino acid composition
Huan Wen Jun-Jie Liu Qian-Zhong Li
Laboratory of Theoretical Biophysics,School of Physical Science and Technology,Inner Mongolia University,Hohhot,China
国际会议
杭州
英文
937-940
2013-03-22（万方平台首次上网日期，不代表论文的发表时间）