Benchmarking MHCflurry, take 2

A few months ago we posted a benchmark of our Class I MHC binding affinity predictor, MHCflurry. That post has useful background if you’re unfamiliar with the problem MHCflurry solves. In our benchmark we found that MHCflurry 0.2.0 (the latest version at the time) underperformed the commonly used NetMHCpan predictor.

We’ve been working hard on this problem since then and we’re happy to report that the current version of MHCflurry (0.9.1) now shows competitive performance with NetMHC and NetMHCpan in two benchmarks we’ve put together. The details are in our preprint on bioRxiv.

MHCflurry is an open-source, easily installed, fast, retrainable, and extendable package for MHC I binding affinity prediction. If your research requires computational epitope discovery, give MHCflurry a try and let us know how it goes!