计算生物学
水准点(测量)
主要组织相容性复合体
班级(哲学)
MHC I级
MHC II级
限制
表位
鉴定(生物学)
结合亲和力
计算机科学
肽
生物
生物信息学
人工智能
遗传学
抗原
生物化学
工程类
受体
机械工程
地理
植物
大地测量学
作者
Peng Wang,John Sidney,Courtney Dow,Bianca R. Mothé,Alessandro Sette,Bjoern Peters
标识
DOI:10.1371/journal.pcbi.1000048
摘要
The identification of MHC class II restricted peptide epitopes is an important goal in immunological research. A number of computational tools have been developed for this purpose, but there is a lack of large-scale systematic evaluation of their performance. Herein, we used a comprehensive dataset consisting of more than 10,000 previously unpublished MHC-peptide binding affinities, 29 peptide/MHC crystal structures, and 664 peptides experimentally tested for CD4+ T cell responses to systematically evaluate the performances of publicly available MHC class II binding prediction tools. While in selected instances the best tools were associated with AUC values up to 0.86, in general, class II predictions did not perform as well as historically noted for class I predictions. It appears that the ability of MHC class II molecules to bind variable length peptides, which requires the correct assignment of peptide binding cores, is a critical factor limiting the performance of existing prediction tools. To improve performance, we implemented a consensus prediction approach that combines methods with top performances. We show that this consensus approach achieved best overall performance. Finally, we make the large datasets used publicly available as a benchmark to facilitate further development of MHC class II binding peptide prediction methods.
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