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Task 3 MHC Class I and II binding affinity

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Ali Haider Bangash edited this page Apr 8, 2020 · 2 revisions

Unfortunately, only a few state of the art MHC class I and II binding prediction tools are available. The most commonly used tool is NetMHCPan I / II, which is unfortunately not open source and more or less proprietary. However, in the recent 2-3 years a few tools were released, which are open source, Python based, have Conda packages, have the same prediction performance as NetMHCPan and are actually way faster.

Our candidates are:

  1. MHCFlurry for class I prediction

The starter code for MHC Class 1 prediction using MHCFlurry library

  1. MHCNuggets for class I and class II

However, since both tools aren't that easily integrated into other workflows, they were integrated into Fred2 and are part of the EpitopePrediction classes. Big drawback: Fred2 requires python2, since it's not really maintained anymore. Hence, if we want to stick to Python 3 and we should, then we have to reimplement the interfacing ourselves. Not difficult, but wastes a little bit of time.

Reference papers:

  1. NetMHCPan4.0
  2. MHCFlurry
  3. MHCNuggets

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