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