• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>American Journal of Bioinformatics Research >On Predicting Conformational B-cell Epitopes: a Comparative Study and a New Model
【24h】

On Predicting Conformational B-cell Epitopes: a Comparative Study and a New Model

机译：关于预测构象性B细胞表位：比较研究和新模型

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Identification of conformational B-cell epitopes is considered the crucial step in designing effective peptide vaccines against pathogens. Computer based methods play an important role in this process as the actual experimental determination of epitopes is very expensive in terms of cost and time. In this paper, we have carried out a comparative study and discussions for different methods based on the two major computational approaches for predicting conformational B-cell epitopes: sequence- based and structure- based approaches. As a result of this study, we developed a novel computational method “CBCPRED” to predict conformational B-cell epitope residues from the target antigen structure by combining support vector machine model with protein structural features and the propensity scores of amino acid physico – chemical properties. Using fivefold cross validation and leave-one-out cross validation techniques on the 75 antigen structures of the Discotope dataset, CBCPRED achieves an area under receiver operator characteristics curve (AUC) of 0.818 and 0.859, respectively. We benchmark “CBCPRED” on a more recent benchmark (Ponomarenko et al. 2007) dataset after removing antigens sequence redundancy where no two antigen sequences have more than 40% sequence identity, achieving AUC of 0.747. CBCPRED is available at http://www.fci.cu.edu.eg:8080/CBCPRED/predict.html.
机译：构象B细胞表位的鉴定被认为是设计针对病原体的有效肽疫苗的关键步骤。基于计算机的方法在此过程中起着重要作用，因为就成本和时间而言，对表位的实际实验确定非常昂贵。在本文中，我们基于两种主要的预测构象B细胞表位的计算方法，对不同方法进行了比较研究和讨论：基于序列的方法和基于结构的方法。这项研究的结果是，我们开发了一种新的计算方法“ CBCPRED”，通过将支持向量机模型与蛋白质结构特征以及氨基酸理化性质的倾向得分相结合，可以从靶抗原结构预测构象B细胞表位残基。在Discotope数据集的75种抗原结构上使用五重交叉验证和留一法交叉验证技术，CBCPRED分别获得了接收者操作员特征曲线（AUC）下方的面积0.818和0.859。去除抗原序列冗余后，我们在较新的基准（Ponomarenko等，2007）数据集上对“ CBCPRED”进行了基准测试，其中两个抗原序列的序列同一性均不超过40％，AUC为0.747。 CBCPRED可从http://www.fci.cu.edu.eg:8080/CBCPRED/predict.html获得。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号