MHC-Ⅱ类抗原表位预测软件的对比评价

Comparative Assessment of Different Softwares for MHC-Ⅱ Antigen Epitope Prediction

比较不同MHC-Ⅱ类抗原表位预测软件的优缺点,为后续应用提供依据。在众多HLA-Ⅱ类抗原表位中,选取HLA-DR的6个表位(DRB1*0101,0301,0401,0701,1101和1501)为代表,选取MHCBN数据库中的309条已知抗原表位的肽链为待测肽链。使用近年来常用的7个表位预测软件,根据不同软件的临界值确定入选结果数据,比较各软件所得结果与已有的实验结果之间的差距以确定其优劣。综合7个软件预测结果进行评价,得出NetMHCⅡ和NetMHCⅡpan所得结果准确率最高。可以用NetMHCⅡpan及NetMHCⅡ进行MHC-Ⅱ类分子抗原表位预测。不同软件HLA的各个亚型的预测所得指标不一致,提示综合运用不同软件对多肽表位进行预测十分必要。

To compare different softwares on the prediction efficacy of MHC-Ⅱ epitopes.From a number of HLA class Ⅱ subtypes,six HLA-DR loci（DRB1＊0101,0301,0401,0701,1101 and 1501） were selected as representative HLA.309 peptides were chosen from MHCBN database as testers,of which the epitopes were well-studied by former experiments and classifled into four binding groups.Seven commonly used epitope prediction softwares were applied on the peptides and the binding data of each peptide were obtained by each software.The experimental data and software data of all peptides were compared in parellel.Five accuracy index were used to evaluate the software.The results showed that each software selected has made full epitope prediction on all peptides and HLA loci.However,the epitope predicting results from different softwares were inconsistent on each single HLA loci.The pooled results by each sofeware showed that the NetMHCⅡ and NetMHCⅡpan produced the highest accuracy to predict MHC-Ⅱ antigen epitopes. NetMHCⅡpan and NetMHCⅡ would be the best in the prediction of MHC class Ⅱ binding epitopes.Inconsistent results by different software implies that it is necessary to use different softwares to predict MHC-Ⅱ antigen epitopes.