期刊
ANALYTICAL BIOCHEMISTRY
卷 436, 期 2, 页码 168-177出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ab.2013.01.019
关键词
Antimicrobial peptide; Pseudo amino acid composition; Physicochemical properties; Fuzzy K-nearest neighbor; Multi-label classification
资金
- National Natural Science Foundation of China [60961003, 6121027, 31260273]
- Chinese Ministry of Education [210116]
- Province National Natural Science Foundation of JiangXi [2010GZS0122, 20114BAB211013, 20122BAB201020]
- Department of Education of JiangXi Province [KJLD12083, GJJ12490]
- Jiangxi Provincial Foreign Scientific and Technological Cooperation Project [20120 BDH80023]
- JiangXi Provincial Foundation for Leaders of Disciplines in Science [20113BCB22008]
Antimicrobial peptides (AMPs), also called host defense peptides, are an evolutionarily conserved component of the innate immune response and are found among all classes of life. According to their special functions, AMPs are generally classified into ten categories: Antibacterial Peptides, Anticancer/tumor Peptides, Antifungal Peptides, Anti-HIV Peptides, Antiviral Peptides, Antiparasital Peptides, Anti-protist Peptides, AMPs with Chemotactic Activity, Insecticidal Peptides, and Spermicidal Peptides. Given a query peptide, how can we identify whether it is an AMP or non-AMP? If it is, can we identify which functional type or types it belong to? Particularly, how can we deal with the multi-type problem since an AMP may belong to two or more functional types? To address these problems, which are obviously very important to both basic research and drug development, a multi-label classifier was developed based on the pseudo amino acid composition (PseAAC) and fuzzy K-nearest neighbor (FKNN) algorithm, where the components of PseAAC were featured by incorporating five physicochemical properties. The novel classifier is called iAMP-2L, where 2L means that it is a 2-level predictor. The 1st-level is to answer the 1st question above, while the 2nd-level is to answer the 2nd and 3rd questions that are beyond the reach of any existing methods in this area. For the conveniences of users, a user-friendly web-server for iAMP-2L was established at http://www.jci-bioinfo.cn/iAMP-2L. (C) 2013 Elsevier Inc. All rights reserved.
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