Predicting the protein SUMO modification sites based on Properties Sequential Forward Selection (PSFS) |
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Authors: | Liu Boshu Li Sujun Wang Yinglin Lu Lin Li Yixue Cai Yudong |
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Institution: | a CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China b Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, China c School of Software, Shanghai Jiao Tong University, China |
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Abstract: | Protein SUMO modification is an important post-translational modification and the optimization of prediction methods remains a challenge. Here, by using Support Vector Machines algorithm (SVM), a novel computational method was developed for SUMO modification site prediction based on Sequential Forward Selection (SFS) of hundreds of amino acid properties, which are collected by Amino Acid Index database (http://www.genome.jp/aaindex). Our method also compares with the 0/1 system, in which the 20 amino acids are represented by 20-dimensional vectors (A = 00000000000000000001, C = 00000000000000000010 and so on). The overall accuracy of leave-one-out cross-validation for our method reaches 89.18%, which is higher than 0/1 system. It indicated that the SUMO modification prediction process is highly related to the amino acid property and this approach here provide a helpful tool for further investigation of the SUMO modification and identification of sumoylation sites in proteins. The software is available at http://www.biosino.org/sumo. |
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Keywords: | Prediction SUMO SVM AAindex Sequential Forward Selection (SFS) Sumoylation |
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