BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity

Lian Wang^{a, #},
Danling Pan^{a, #},
Xihao Hu^{a, #},
Jinyu Xiao^a,
Yangyang Gao^a,
Huifang Zhang^a,
Yan Zhang^a,
Juan Liu^{a
, ,},
Shanfeng Zhu^{b, c
, ,}

a.
School of Computer, Wuhan University, Wuhan 430079, China
b.
School of Computer Science, Fudan University, Shanghai 200433, China
c.
Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, 200433, China

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Corresponding author: E-mail address: liujuan@whu.edu.cn (Juan Liu); E-mail address: zhusf@fudan.edu.cn (Shanfeng Zhu)

These authors contributed equally to this work.

摘要

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Abstract: 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.
- MHC II /
- MHC-peptide binding predictions /
- web server
These authors contributed equally to this work.
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参考文献(20)

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doi: 10.1016/S1673-8527(08)60117-4

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BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity

Corresponding author: E-mail address: liujuan@whu.edu.cn (Juan Liu); E-mail address: zhusf@fudan.edu.cn (Shanfeng Zhu)

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doi: 10.1016/S1673-8527(08)60117-4

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BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity

Corresponding author: E-mail address: liujuan@whu.edu.cn (Juan Liu); E-mail address: zhusf@fudan.edu.cn (Shanfeng Zhu)

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