BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity |
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| Authors: | Lian Wang Danling Pan Xihao Hu Jinyu Xiao Yangyang Gao Huifang Zhang Yan Zhang Juan Liu Shanfeng Zhu |
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| Affiliation: | 1. Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA;2. Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN 55905, USA;3. Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA;1. Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Japan;2. Department of Laboratory Medicine, Shinshu University Hospital, Japan;1. The Scripps Research Institute, La Jolla, CA, USA;2. University of California, Los Angeles (UCLA), Los Angeles, CA, USA;3. Fox Chase Cancer Center, Philadelphia, PA, USA;4. Laboratory of Cell Biology, Ariel University, Ariel, Israel;5. Mayo Clinic, Rochester, MN, USA |
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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. |
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| Keywords: | MHC Ⅱ MHC-peptide binding predictions web server |
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