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FreshAirTonight / af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
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Can af2complex predict the impact of missense mutations on structure and interaction? and how to run af2complex in docker? #5

Open joelive opened 2 years ago

joelive commented 2 years ago

1.According to this paper Buel, G.R., Walters, K.J. Can AlphaFold2 predict the impact of missense mutations on structure?. Nat Struct Mol Biol 29, 1–2 (2022). https://doi.org/10.1038/s41594-021-00714-2, AlphaFold2 does not perform well on predicting the impact of missense mutations on structure. Can af2complex predict the impact of missense mutations on structure and interaction?

2.After cloning alphafold, in which directory should I clone af2complex? the root dir of alphafold?

3.I used to run alpha fold through run_docker.py is it possible to run af2complex using docker?

FreshAirTonight commented 2 years ago

To answer your questions:

  1. Since AF2Complex uses the same neural network models as AF2, it very likely has similar limitations as AF2. I think that it is a long shot to model missense effects on structures accurately in general. This topic needs further investigation.
  2. I recommend that you place AF2Complex code in a folder separate from AF2, because operates independently from AF2's source code. It only needs the python environment that you had set up for AF2.
  3. I have not tested the code with a docker image, but it has been used with a Singularity image. I think that you should be able to run it with docker as well. Alternatively, you may set it up within a anaconda environment w/o using any image.