Predicting linear B-cell epitopes using amino acid anchoring pair composition

Weike Shen, Yuan Cao, Lei Cha, Xufei Zhang, Xiaomin Ying, Wei Zhang, Kun Ge, Wuju Li, Li Zhong

Accurate identification of linear B-cell epitopes plays an important role in peptide vaccine designs, immunodiagnosis, and antibody productions. Although several prediction methods have been reported, unsatisfied accuracy has limited the broad usages in linear B-cell epitope prediction. Therefore, developing a reliable model with significant improvement on prediction accuracy is highly desirable. In this study, we developed a novel model for prediction of linear B-cell epitopes, APCpred, which was derived from the combination of amino acid anchoring pair composition (APC) and Support Vector Machine (SVM) methods. Systematic comparisons with the existing prediction models demonstrated that APCpred method significantly improved the prediction accuracy both in fivefold cross-validation of training datasets and in independent blind datasets. In the fivefold cross-validation test with Chen872 dataset at window size of 20, APCpred achieved AUC of 0.809 and accuracy of 72.94%, which was much more accurate than the existing models, e.g., Bayesb, Chen's AAP methods and the enhanced combination method of AAP with five AP scales. For the fivefold cross-validation test with ABC16 dataset, APCpred achieved an improved AUC of 0.794 and ACC of 73.00% at window size of 16, and attained an AUC of 0.748 and ACC of 67.96% on Blind387 dataset after being trained with ABC16 dataset. Trained with Lbtope_Confirm dataset, APCpred achieved an increased Acc of 55.09% on FBC934 dataset. Within sequence window sizes from 12 to 20, APCpred final model on homology-reduced dataset achieved an optimal AUC of 0.748 and ACC of 68.43% in fivefold cross-validation at the window size of 20. APCpred model demonstrated a significant improvement in predicting linear B-cell epitopes using the features of amino acid anchoring pair composition (APC). Based on our study, a webserver has been developed for on-line prediction of linear B-cell epitopes, which is a free access at: http:/ccb.bmi.ac.cn/APCpred/.