BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity.
Effective identification of major histocompatibility complex (MHC) molecules restricted peptides is a critical step in discovering immune epitopes. Although many online servers have been built to predict class II MHC-peptide binding affinity, they have been trained on different datasets, and thus fail in providing a unified comparison of various methods. In this paper, we present our implementation of seven popular predictive methods, namely SMM-align, ARB, SVR-pairwise, Gibbs sampler, ProPred, LP-top2, and MHCPred, on a single web server named BiodMHC (http://biod.whu.edu.cn/BiodMHC/index.html, the software is available upon request). Using a standard measure of AUC (Area Under the receiver operating characteristic Curves), we compare these methods by means of not only cross validation but also prediction on independent test datasets. We find that SMM-align, ProPred, SVR-pairwise, ARB, and Gibbs sampler are the five best-performing methods. For the binding affinity prediction of class II MHC-peptide, BiodMHC provides a convenient online platform for researchers to obtain binding information simultaneously using various methods.
Wang
Lian
L
School of Computer, Wuhan University, Wuhan 430079, China.
Pan
Danling
D
Hu
Xihao
X
Xiao
Jinyu
J
Gao
Yangyang
Y
Zhang
Huifang
H
Zhang
Yan
Y
Liu
Juan
J
Zhu
Shanfeng
S
D000818:Animals; D030562:Databases, Protein; D000949:Histocompatibility Antigens Class II / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D020407:Internet; D009862:Online Systems; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D012984:Software
D000949:Histocompatibility Antigens Class II; D010455:Peptides