Transmembrane Domain Adaptation

BioMemPhys-FAU / domhmm

Open source package to identify nano- and microdomains in Molecular Dynamics simulations of bio-membranes.

https://www.biomemphys.nat.fau.de

GNU General Public License v2.0

0 stars 0 forks source link

Transmembrane Domain Adaptation #45

Closed yusuferentunc closed 2 weeks ago

yusuferentunc commented 1 month ago

If there are transmembrane protein in simulation, it will efect calculation of area per lipid.
Protein's backbones that is close to leaflets needs to be included into area per lipid calculation but excluded from HMM model training.
User will provide selection of atoms to be included into area per lipid calculation just like in leaflet logic.

Late work todo list

[x] ~Add unit tests~ (Tests will be add in future for pull request acceptance pipeline)
[x] Update documentation (done at #49)

yusuferentunc commented 1 month ago

Would we also need to use transmembrane domain area per lipid results in weight matrix calculation? @m-a-r-i-u-s

m-a-r-i-u-s commented 1 month ago

Would we also need to use transmembrane domain area per lipid results in weight matrix calculation? @m-a-r-i-u-s

I don't think so. The influence of the TMD is already present, since the distances/edges are coming from the Voronoi diagram with the protein included. For later steps (e.g., Getis Ord) the protein should not be used...At least I cannot think of an useful incorporation right now...