iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types
iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types
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iAMP-2L：用于识别抗菌肽及其功能类型的两级多标签分类器
DOI：
10.1016/j.ab.2013.01.019
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发表时间：
2013-05-15
影响因子：
2.9
通讯作者：
Chou, Kuo-Chen
中科院分区：
文献类型：
--
作者：
Xiao, Xuan;Wang, Pu;Chou, Kuo-Chen
抗菌肽（Antimicrobial peptides, AMPs）也被称为宿主防御肽，是先天免疫反应的一种进化保守成分，存在于所有生命类别中。根据抗菌肽的特殊功能，将其分为抗菌肽、抗癌肽、抗真菌肽、抗hiv肽、抗病毒肽、抗寄生虫肽、抗原生生物肽、具有趋化活性的抗菌肽、杀虫肽和杀精肽等十大类。给定一个查询肽，我们如何识别它是AMP还是非AMP？如果是，我们能确定它属于哪个功能类型吗？特别是，由于AMP可能属于两个或多个功能类型，我们如何处理多类型问题？为了解决这些对基础研究和药物开发都非常重要的问题，基于伪氨基酸组成（PseAAC）和模糊k近邻（FKNN）算法开发了一种多标签分类器，其中PseAAC的成分包含五种物理化学性质。新的分类器被称为iAMP-2L，其中“2L”意味着它是一个2级预测器。第一级是回答上面的第一个问题，而第二级是回答这个领域的任何现有方法都无法解决的第二和第三个问题。为了方便用户使用，在http://www.jci-bioinfo.cn/iAMP-2L上建立了一个用户友好的iAMP-2L web服务器。(C) 2013爱思唯尔公司版权所有。
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.