Hi,
This is unrelated to PyMol, but I just wanted to spam the community to see
what they think about different protein parameters. Let me know if this
sort of question is inappropriate for the forum.
I have thousands of randomly generated 7 amino acid peptide sequences that
are within a virus. As we subject this virus to reproduction selective
pressure in cell lines, we get back functional viruses with certain 7 amino
acid sequences, while most random sequences are null mutations. So I am now
testing the the positive sequences to see what they have in common, or what
is most important.
I am doing this with a likely structural sequence and a likely surface
sequence.
So far I have these params from http://web.expasy.org/protparam/ and ConSurf
1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations
Do any of you protein experts know of other parameters that I could be
testing? Maybe something like Phi-value analysis?
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