How to differentiate ordered and disordered protein complexes in pdb?
Based on the stoichiometry, we can download heteromers(I need stoichiometery AB) from pdb. But I think, if we download like this, some disordered protein complexes are also include in the list. I need only ordered protein complexes. Are there any way to get ordered protein complexes from pdb?
• 2,228 views
•
link
updated
by
Ram
•
written
by
andrew.benny •
•
written
by
andrew.benny •
1 answer
Just an idea, but you have several options:
- You can look for the SCOP/CATH classifications for disordered proteins and rule out those complexes that match them.
- You can look at the DSSP annotation for each protein and sort of quantify the secondary structures. If above a certain threshold, consider them disordered and ignore them.
- Cross information from disorder databases (DisPro) with RCSB and filter the common entries.
• 0 views
•
link
updated
by
Ram
•
written
by
João Rodrigues
•
written
by
João Rodrigues
Log in to answer this question.
More posts like this
-
PDBePISA calls monomers heteromers, how can one programmatically correct this downstream
written by plberry •
-
Intrinsically disordered region(IDR) or Intrinsically disordered Protein(IDP)
written by dachi •
-
How download a sequence fasta from PDB using biopython / python?
written by thayana.vt •
-
How to estimate the stability of a protein complex?
written by Qroid •
-
Batch convert gene numbers (ordered locus names) to protein IDs
written by Qroid •
-
How to get fully ordered proteins from PDB
written by Behoston •
-
Finding Structures Of Protein Complexes!
written by kandoigaurav
-
How Do I Download Protein Monomers From Pdb?
written by kadhar •
-
Good Multiple Sequence Alignment Tool For Ordered/Disordered Proteins
written by miquelduranfrigola
-
Functional Classification Of Protein Complexes
written by Reyhaneh
