Is it significant the overlapping of one residue for MHC binding?

richelbilderbeek commented 3 years ago

From a reviewer:

Is it significant the overlapping of one residue for MHC binding? Why not consider only those peptides that are really predicted and analyze them if they are really found in experimental data? Contribution of one residue of the TMH to the ligand is almost anecdotic even more if this contribution mainly affects N or C-terminal positions. It is logically to see these residues located near outside the lipid bilayer because they are more “available” to be processed independently of what the mechanistic process is. It would be nice to saw how the TMH contributes to every position of the ligand predicted compared to those experimentally confirmed.

[ ] Richel: check with 2 AAs overlap, demonstrate that this does not matter, use one haplotype :-)
[ ] Richel: Less overlap means less TMH-derived epitopes, hence lower statistical power

richelbilderbeek commented 3 years ago

Adapted bbbq_1_smart with this commit

richelbilderbeek commented 3 years ago

It is in the manuscript, except that the figures are identical :-/

Screenshot from 2021-11-04 10-39-41