Question: Amino acid distribution along the transmembrane
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gravatar for rkmishra16
3.0 years ago by
rkmishra160
rkmishra160 wrote:

Dear all, I want to calculate frequency of various residues in transmembrane protein. For this, I have to align the membrane protein in the bilayer so that z-axis is parallel to bilayer normal. Then, i have to calculate frequency of any residue at a particular distance in Å from the centre of bilayer(z = 0). This seems to be normal practice for aligning transmembrane proteins after getting coordinates from PDB structure. Could someone please guide me as to how this can be done in python or Bio-python?

alignment • 831 views
ADD COMMENTlink written 3.0 years ago by rkmishra160

Do you want to know topology of the TMs proteins? Along with that know amino acid distribution in specific membranes?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Bioinformatics_NewComer320

Thanks. I know the topology from structures. I just want to calculate amino acid frequency along the transmembrane by structural alignment method (along the z-axis).

ADD REPLYlink written 3.0 years ago by rkmishra160
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