Epitope Prediction Based on Random Peptide Library Screening: Benchmark Dataset and Prediction Tools Evaluation

Pingping Sun, Wenhan Chen, Yanxin Huang, Hongyan Wang, Zhiqiang Ma, Yinghua Lv
2011 Molecules  
Epitope prediction based on random peptide library screening has become a focus as a promising method in immunoinformatics research. Some novel software and web-based servers have been proposed in recent years and have succeeded in given test cases. However, since the number of available mimotopes with the relevant structure of template-target complex is limited, a systematic evaluation of these methods is still absent. In this study, a new benchmark dataset was defined. Using this benchmark
more » ... g this benchmark dataset and a representative dataset, five examples of the most popular epitope prediction software products which are based on random peptide library screening have been evaluated. Using the benchmark dataset, in no method did performance exceed a 0.42 precision and 0.37 sensitivity, and the MCC scores suggest that the epitope prediction results of these software programs are greater than random prediction about 0.09-0.13; while using the representative dataset, most of the values of these performance measures are slightly improved, but the overall performance is still not satisfactory. Many test cases in the benchmark dataset cannot be applied to these pieces of software due to software limitations. Moreover chances are that these software products are overfitted to the small dataset and OPEN ACCESS Molecules 2011, 16 4972 will fail in other cases. Therefore finding the correlation between mimotopes and genuine epitope residues is still far from resolved and much larger dataset for mimotope-based epitope prediction is desirable.
doi:10.3390/molecules16064971 pmid:21681149 fatcat:eg26v5u335dh5czex7epsinevy