Zuo Yongchun, Lv Yang, Wei Zhuying, Yang Lei, Li Guangpeng, Fan Guoliang
The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, College of life sciences, Inner Mongolia University, Hohhot, China.
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
PLoS One. 2015 Dec 29;10(12):e0145541. doi: 10.1371/journal.pone.0145541. eCollection 2015.
Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans. To identify specific defensins as interesting antifungal leads, in this study, we constructed a more rigorous benchmark dataset and the iDPF-PseRAAAC server was developed to predict the defensin family and subfamily. Using reduced dipeptide compositions were used, the overall accuracy of proposed method increased to 95.10% for the defensin family, and 98.39% for the vertebrate subfamily, which is higher than the accuracy from other methods. The jackknife test shows that more than 4% improvement was obtained comparing with the previous method. A free online server was further established for the convenience of most experimental scientists at http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp. A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful high-throughput tool for both basic research and drug design.
防御素作为最丰富的一类抗菌肽，是大多数生物从低等生物到人类进化过程中固有免疫的重要组成部分。为了鉴定出作为有趣抗真菌先导物的特定防御素，在本研究中，我们构建了一个更严格的基准数据集，并开发了iDPF-PseRAAAC服务器来预测防御素家族和亚家族。使用简化的二肽组成，所提出方法对防御素家族的总体准确率提高到了95.10%，对脊椎动物亚家族的准确率提高到了98.39%，高于其他方法的准确率。留一法检验表明，与之前的方法相比，准确率提高了4%以上。为方便大多数实验科学家，还在http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp建立了一个免费的在线服务器。提供了一个友好的指南来描述如何使用该网络服务器。我们预计iDPF-PseRAAAC可能会成为基础研究和药物设计中一个有用的高通量工具。
