I have observed a 50 conformer for a protein by experimental method of NMR solution. How to choose the best conformer for simulation study?
You have to select the conformation, which has been associated with the binding to your ligand. For instance, an inward-facing apo-P-gp conformation was chosen as a reliable drug-binding model. This conformation represents an initial stage of the transport cycle that is competent for inhibitor or substrate binding (Shityakov et al., 2014).
I know the binding region of the drug and the essential amino acids participating during the binding, So according to your suggested method I have to select that conformation of the protein in which these essential amino acids will interact with drug.
you can to order the conformations by Boltzmann distribution energy...
I think the fairest way, if I understand the question, is to select the conformation closest to the NMR ensemble average (e.g. the one with the lowest RMSD to the average).
You can select the lowest energy but that may not be representative. You can also generate a mean structure by averaging over all conformations but that will have all kinds of problems due to the averaging. If you refine the mean structure it will no longer be an average ...
In many cases the best conformer is mentioned by the authors in the PDB file itself
for example
consider PDB id 1kwd which has 16 conformers (models) among which the 7th conformer is the best representative conformer as mentioned in the "REMARK 210" by the statement "BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 7"
If the best conformer is not mentioned (or mentioned as "NULL") then you may take the first model to continue your study.
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