How to loop through to get the polypeptide sequences of multiple structures using Biopython Bio.PDB module.

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 python polypeptide bio.pdb

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written 7.5 years ago by M.O.L.S •

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.

• 1 views • link

written 7.5 years ago by Joe

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