The most common reason for run-time errors for the class I and II binding prediction tools is that the user has input too large a data set for the web server to handle. Suggested work-arounds to this problem can be found at http://help.iedb.org/entries/108930096-MHC-class-I-binding-prediction-Internal-Server-Error for class I and at http://help.iedb.org/entries/106939226-MHC-II-Epitope-Prediction-Internal-Server-Error- for class II.
The capability to handle larger data sets should be deployed by the end of 2016.
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