EOM as a dimer with no PDBs

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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akoeni01
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EOM as a dimer with no PDBs

#1 Post by akoeni01 » 2017.10.27 17:41

My protein elutes from size exclusion as a dimer so I want to input P2 symmetry, however when you assume an oligomer it requires a PDB for at least one of the domains. If I don't have a structure for any part of this protein is there a way to still run EOM assuming P2 symmetry?

Nyshae
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Re: EOM as a dimer with no PDBs

#2 Post by Nyshae » 2017.11.01 12:45

You can do that only if your protein is intrinsically unfolded. If it is just that you don't know the structure (but it still has one), you might either want to use models based on your sequence and a homolog structure (made for example with SWISS model) or use another program (e.g. DAMMIN-F).

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AL
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use a very short dimer

#3 Post by AL » 2017.11.06 12:38

If you know the dimerization interface you may use a very short dimer that consists of just a few residues.
You may also want to try EOM without symmetry (just provide the same sequence twice).

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