I want to compare the protein dynamics
) pH 7 versus pH 3, or
) wild type versus mutant
The protein will have slightly different number of atoms at each condition, due to protonation or mutation. The alternative is to only consider the alpha-carbon atoms, but this will lose significant amount of information (e.g. side chain, salt bridge).
Is there a way in molecular dynamics to extract features from ensembles of different number of atoms?
In case of pH, you can try try to look at the protein without protons. This can even work for hydrogen bond analysis (just look at the distances between heavy atoms to get an initial idea).
For mutations, I think there is no universal recipe.
A lot of methods in protein-related machine learning is now based on residue-wise contact or distance matrices. That's something that should remain fixed regardless of mutations or protonation changes, and can be used with all image analysis methods (including e.g. CNNs).
Try gRINN: https://academic.oup.com/nar/article/46/W1/W554/5003454
I'd be happy to assist you in case you need any help using the tool.
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