EpiJen: a server for multistep T cell epitope prediction.
EpiJen: a server for multistep T cell epitope prediction.
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DOI：
10.1186/1471-2105-7-131
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发表时间：
2006-03-13
影响因子：
3
通讯作者：
Flower DR
中科院分区：
文献类型：
--
作者：
Doytchinova IA;Guan P;Flower DR
MHC I类配体的主要加工途径包括蛋白酶体降解蛋白质，然后由抗原加工相关转运体（TAP）将产物运输到内质网（ER），在内质网中，肽与MHC I类分子结合，然后由MHC呈现在细胞表面。整个过程是用一种综合方法来建模的，我们称之为EpiJen。EpiJen基于定量矩阵，通过加性方法推导，并依次应用于选择表位。EpiJen可以在网上免费获得。为了确定表位，源蛋白经过四个步骤：蛋白酶体切割、TAP运输、MHC结合和表位选择。在每个阶段，不同比例的非表位被淘汰。如外部验证所示，最终的肽集不超过整个蛋白质序列的5%，并将包含85%的真实表位。与其他综合方法（NetCTL， WAPP和SMM）相比，EpiJen表现最好，预测了本研究中使用的99个HIV表位中的61个。EpiJen是一种可靠的T细胞表位预测多步算法，属于新一代的计算机T细胞表位鉴定方法。这些方法旨在通过提高表位预测的成功率来减少后续的实验工作。
The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endoplasmic reticulum (ER), where peptides are bound by MHC class I molecules, and then presented on the cell surface by MHCs. The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online. To identify epitopes, a source protein is passed through four steps: proteasome cleavage, TAP transport, MHC binding and epitope selection. At each stage, different proportions of non-epitopes are eliminated. The final set of peptides represents no more than 5% of the whole protein sequence and will contain 85% of the true epitopes, as indicated by external validation. Compared to other integrated methods (NetCTL, WAPP and SMM), EpiJen performs best, predicting 61 of the 99 HIV epitopes used in this study. EpiJen is a reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent experimental work by improving the success rate of epitope prediction.
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影响因子：
2.7
作者：
Bisset, Leslie R.;Fierz, Walter
通讯作者：
Fierz, Walter
影响因子：
3.5
作者：
Doytchinova, IA;Flower, DR
通讯作者：
Flower, DR
影响因子：
4.8
作者：
Beninga, J;Rock, KL;Goldberg, AL
通讯作者：
Goldberg, AL
DOI：
10.1021/ci00010a010
发表时间：
1992-11-01
期刊：
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
影响因子：
--
作者：
BARNARD, JM;DOWNS, GM
通讯作者：
DOWNS, GM
影响因子：
8
作者：
Bradley, AP
通讯作者：
Bradley, AP