Le 16/09/2020 à 06:34, Navid
Shervani-Tabar a écrit :
Dear Navid,Thanks, Stéphane! Can you by any chance point me to an example with either of them? (It seems biopython is more relevant for my purpose, which is to load positions and dihedral angles for a large dataset and add conformation type as a label to each one, but I can't find anything in its tutorials). Thanks again!
Best,Navid
If you want to use command-line, then biopython may do the trick.
I also forgot to talk also about MDanalysis for which a binding to rdkit was developped this year
(https://www.mdanalysis.org/2020/08/29/gsoc-report-cbouy/).
The problem with biopython is that its documentation is targeting bioinformaticians,
and thus not always clear :-)
If you go for it (and I recommend it), then you can look at the Bio.PDB module which has his own documentation:
https://biopython.org/docs/1.75/api/Bio.PDB.html
What you want to do is bulding a polypeptide chain "from scratch" from a sequence:
https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
https://biopython.org/docs/1.75/api/Bio.PDB.StructureBuilder.html
Briefly:
1 - create a CaPPBuilder or a structure object if you want to start from scratch
from Bio.PDB.Polypeptide import PPBuilderppb = CaPPBuilder()
See also https://biopython.org/docs/1.75/api/Bio.PDB.Structure.html
2 - load an existing pdb file (the one containing your dihedral
angles):parser = PDB.PDBParser()
newpdb = parser.get_structure('theNew', filename)
pp=ppb.build_peptides(newpdb)
(get the resulting sequence)
seq=pp[0].get_sequence()
3 - write out the new pdb
io = PDBIO() io.set_structure(s) io.save("out.pdb") If more is required, look at the reference papers and/or ask the (low traffic) biopython mailing list. Best, Stéphane PS: keeping the discussion on the list since it may help others (and they'll probably complete my answer).
-- Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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