The last email have some errors please see this one.
In my system ,the loop is part of the active pocket of the protein. when the ligand is absent, the loop is disordered. if the ligand is present , the loop can transform into helix. In order to simulate the disordered loop transform into helix , i should build a model that the ligand and cofactor are in the disoreded loop site. In my system, there is a NAD+ cofactor in the active site and interact with the ligand.when the ligand and cofactor NAD+ coexist, the disordered loop can transform into helix. In the PDB(protein date base) i find the complex with the liand,NAD+ and the state of the loop is helix. i also find a structure of the protein without the liand, NAD+ and the state of the loop is disordered. The sequences similarity of the two structure is 100% and the RMSD between the two structures of the protein is 0.275 . i don't know how to build a model that the protein, NAD+ and ligand coexsit and the loop of protein is disordered. could give me some advice and tell me how to do it detailed? thank you very much.
On 4/29/13 8:25 PM, aixintiankong wrote: > i don't know how to build a model that the protein, NAD+ and ligand > coexsit and the loop of protein is disordered.
One way to do this would be to align your model sequence with the first template (loop is helix) for the entire sequence except the loop, and the second template (loop is disordered) for the loop: http://salilab.org/modeller/9.11/FAQ.html#1
Another way would be to just use the first template, and just unalign the loop so Modeller builds it without template information: http://salilab.org/modeller/9.11/FAQ.html#2
Ben Webb, Modeller Caretaker