title: Prediction of antimicrobial peptides based on sequence alignment and feature selection methods.
abstract: Antimicrobial peptides (AMPs) represent a class of natural peptides that form a part of the innate immune system, and this kind of 'nature's antibiotics' is quite promising for solving the problem of increasing antibiotic resistance. In view of this, it is highly desired to develop an effective computational method for accurately predicting novel AMPs because it can provide us with more candidates and useful insights for drug design. In this study, a new method for predicting AMPs was implemented by integrating the sequence alignment method and the feature selection method. It was observed that, the overall jackknife success rate by the new predictor on a newly constructed benchmark dataset was over 80.23%, and the Mathews correlation coefficient is 0.73, indicating a good prediction. Moreover, it is indicated by an in-depth feature analysis that the results are quite consistent with the previously known knowledge that some amino acids are preferential in AMPs and that these amino acids do play an important role for the antimicrobial activity. For the convenience of most experimental scientists who want to use the prediction method without the interest to follow the mathematical details, a user-friendly web-server is provided at http://amp.biosino.org/.
authors.affiliation: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Wang
authors.forename: Lele
authors.initials: L
authors.lastname: Hu
authors.forename: Guiyou
authors.initials: G
authors.lastname: Liu
authors.forename: Nan
authors.initials: N
authors.lastname: Jiang
authors.forename: Xiaoyun
authors.initials: X
authors.lastname: Chen
authors.forename: Jianyong
authors.initials: J
authors.lastname: Xu
authors.forename: Wen
authors.initials: W
authors.lastname: Zheng
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Ming
authors.initials: M
authors.lastname: Tan
authors.forename: Zugen
authors.initials: Z
authors.lastname: Chen
authors.forename: Hui
authors.initials: H
authors.lastname: Song
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D000890:Anti-Infective Agents / Q000737:chemistry* / Q000494:pharmacology; D010455:Peptides / Q000737:chemistry* / Q000494:pharmacology; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D000890:Anti-Infective Agents; D010455:Peptides