Hello,
First of all, thanks ITASSER for giving a strong support for my research in past years. I really appreciate it.
Recently I retrieved my protein model using ITASSER and COACH, in which catalytic residues are positioned in the way that productive reaction is likely to occur. And also a cofactor (NADP+) is bound in a reasonable conformation.
Now I would like to replace NADPH instead of NADP in the site, because NADPH is the reactant that transfers the hydride to substrate. So the model with NADPH bound is more realistic to the chemical reaction that the enzyme is going to catalyze, and later I will use this modified model for docking. Do you have any suggestions on how to make change cofactor, basically adding another hydrogen at C4 on nicotinamide ring. Thank you very much.
Looking forward to hearing from you.
Best,
Chao