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TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition

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Abstract

Antifreeze proteins (AFPs) are indispensable for living organisms to survive in an extremely cold environment and have a variety of potential biotechnological applications. The accurate prediction of antifreeze proteins has become an important issue and is urgently needed. Although considerable progress has been made, AFP prediction is still a challenging problem due to the diversity of species. In this study, we proposed a new sequence-based AFP predictor, called TargetFreeze. TargetFreeze utilizes an enhanced feature representation method that weightedly combines multiple protein features and takes the powerful support vector machine as the prediction engine. Computer experiments on benchmark datasets demonstrate the superiority of the proposed TargetFreeze over most recently released AFP predictors. We also implemented a user-friendly web server, which is openly accessible for academic use and is available at http://csbio.njust.edu.cn/bioinf/TargetFreeze. TargetFreeze supplements existing AFP predictors and will have potential applications in AFP-related biotechnology fields.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 61373062, 61222306, 61202134, and 61233011), the Natural Science Foundation of Jiangsu (No. BK20141403), Jiangsu Postdoctoral Science Foundation (No. 1201027C), the Jiangsu University Graduate Research and Innovation Project (No. KYZZ_0123), the China Postdoctoral Science Foundation (No. 2013M530260, 2014T70526), “The Six Top Talents” of Jiangsu Province (No. 2013-XXRJ-022), the Fundamental Research Funds for the Central Universities (No. 30920130111010).

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Authors and Affiliations

  1. School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing, 210094, China

    Xue He, Ke Han, Jun Hu, Hui Yan, Jing-Yu Yang & Dong-Jun Yu

  2. Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China

    Hong-Bin Shen

  3. Changshu Institute, Nanjing University of Science and Technology, Changshu, 215513, China

    Dong-Jun Yu

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  1. Xue He
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  2. Ke Han
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Correspondence to Dong-Jun Yu.

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He, X., Han, K., Hu, J. et al. TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition. J Membrane Biol 248, 1005–1014 (2015). https://doi.org/10.1007/s00232-015-9811-z

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  • DOI: https://doi.org/10.1007/s00232-015-9811-z

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