How to differentiate ordered and disordered protein complexes in pdb?

Question

[andrew.benny]

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?

Answer 1

[João Rodrigues]

Just an idea, but you have several options:

1. You can look for the SCOP/CATH classifications for disordered proteins and rule out those complexes that match them.
2. 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.
3. Cross information from disorder databases (DisPro) with RCSB and filter the common entries.