How To Find Disordered Residues From A Protein Sequence Using Biopython?

Question

[Mkl]

Hi,

I have a data set which contains 800 protein sequences. I would like to find disordered residues from each sequence. How to find disordered residues in Biopython?

[Peter]

Could you expand your question with some example data? Biopython can read ASTRAL SCOP files and PDB files, so it should be possible. I don't (yet) understand what you are asking for exactly.

[Peter]

Are you trying to read any disorder information in a PDB file explicitly, or infer/predict it from the structure?

[Mkl]

@peter I am trying to import ASTRAL SCOP original-style domain sequences, based on PDB SEQRES records and trying to find disordered residues from it using biopython. Is it possible in Biopython?

[Mkl]

How to parse Astral SCOP PDB files in Biopython?

[Mkl]

@peter I am trying to read PDB_Seqres sequences from SCOP.After this, I can do pairwise sequence alignment using clustalw with Biopython. gaps in the alignment denotes disordered residues.

Answer 1

[Lars Juhl Jensen]

I think you are making a big mistake here by saying it must be done in BioPython. If you want to find disordered regions, you should use whichever prediction method that works the best. If that is not one that is integrated in BioPython, then so be it.

At the moment, I would use IUPred for this problem.

[Lars Juhl Jensen]

I would go a bit further than that Neil. Even if someone has implemented a disorder prediction algorithm in BioPython, you should not use it if it is not as good as the best available method. Your #1 criterion for selecting a method should be how well it does the job, not whether or not it has been implemented in BioPython.

[Peter]

See comments on question itself - @mkl doesn't want to do the prediction in (Bio)python, rather parsing ASTRAL SCOP and/or PDB files for disorder information.

[Mkl]

Thank you for your answer.I know about the disorder prediction softwares.But I am trying to find disordered residues using Biopython.

[Neilfws]

Question is: has someone implemented a disorder prediction algorithm for Biopython? If yes, all well and good. If not, as Lars says, then you should use the best available method.

[Neilfws]

Completely agree Lars.

[Lars Juhl Jensen]

Yes, I see that - but it was not clear from the original question at all.