Dear Theresa,
Use as many prediction softwares as possible. First I would go for
transmembrane topology prediction, try at least tmhmm, dgpred or topcons to
see if they agree on the number of tm's that will be indicative of the
fold. Topcons, octopus, will tell you if there is any re-entrant loop,
One possible outcome is: (a) if the two proteins bind similar ligands and (b)
you know which part of the xray structure of the solved protein is binding the
ligand and (c) you can use this information to tweak the alignment and
determine that there is higher identity/similarity in the ligand bin
: [ccp4bb] Off topic: Homology modeling
Dear all
I am working with a membrane protein without known structure. The closest
protein in PDB has 10% sequence identity/25% similarity to my protein.
What is the best method and software to do homology modeling while I try to get
the crystal? Is the ligand
Dear all
I am working with a membrane protein without known structure. The closest
protein in PDB has 10% sequence identity/25% similarity to my protein.
What is the best method and software to do homology modeling while I try to get
the crystal? Is the ligand binding site prediction reliable?
