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?
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andrew.benny •
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andrew.benny •
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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.
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João Rodrigues
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