Re: [modeller_usage] post translational modification

[Modeller Caretaker <>]

suji george wrote:
> Can Modeller be used to study the effect of post translational
> modification on the structure of protein. For instance if a lysine in
> a protein is modified to carboxymethyllysine. In such situation, can
> the modified template be used for modeling. The model so obtained by
> the alignment of modified protein as template and native protein
> reflect the effect of modification on the structure. Is it necessary
> to consider the modified amonoacid (carboxymethyllysine)as unnatural
> amino acid and modify the charmm topology and parameter files.

Sure, you could build a model using the original structure as a template 
and the modified sequence as the model sequence. For the best results, 
yes, you'd have to add topology and parameters for the modified residue.

	Ben Webb, Modeller Caretaker
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