Question: How to loop through to get the polypeptide sequences of multiple structures using Biopython Bio.PDB module.
0
gravatar for M.O.L.S
9 days ago by
M.O.L.S0
M.O.L.S0 wrote:
structureA = PDBParser().get_structure("2rheH", " 2rheH")
PolypeptideBuilder = PPBuilder()
for pp in PolypeptideBuilder.build_peptides(structureA):
print(pp.get_sequence())

>>> ESVLTQPPSASGTPGQRVTISCTGSATDIGSNSVIWYQQVPGKAPKLLIYYNDLLPSGVSDRFSASKSGTSASLAISGLESEDEADYYCAAWNDSLDEPGFGGGTKLTVLGQPK

structureB = PDBParser().get_structure("3ebxH", "3ebxH") 
PolypeptideBuilder = PPBuilder()
for pp in PolypeptideBuilder.build_peptides(structureB):
print(pp.get_sequence())
>>> RICFNHQSSQPQTTKTCSPGESSCYHKQWSDFRGTIIERGCGCPTVKPGIKLSCCESEVCNN

structureC = PDBParser().get_structure("1fxdH", " 1fxdH")
PolypeptideBuilder = PPBuilder()
for pp in PolypeptideBuilder.build_peptides(structureC):
print(pp.get_sequence())
>>> PIEVNDDCMACEACVEICPDVFEMNEEGDKAVVINPDSDLDCVEEAIDSCPAEAIVRS

I am using Biopython's Bio.PDB to get the protein sequences of PDB files.

This is the code that I have used in order to get three sequences.

I would like to find out if there is a way that I could loop this operation in order to get all three sequences printed out from the three different files at once?

bio.pdb polypeptide bio python • 87 views
ADD COMMENTlink written 9 days ago by M.O.L.S0

Do you actual need peptide chain sequences or do you want the full protein sequence?

The easy way to loop your IDs is just to throw the whole thing inside a loop of names:

for ID in ["2reH", "3ebxH", ...]:
    structure = PDBParser().get_structure(ID, ID)
    PolypeptideBuilder = PPBuilder()
    for pp in PolypeptideBuilder.build_peptides(structure):
    print(pp.get_sequence())

You might want to check out this previous thread.

ADD REPLYlink modified 9 days ago • written 9 days ago by jrj.healey10k
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