Hello all I have a pdb file and coordinate of 13 amino acid (N-terminal arm)are missing in this pdb file.
Is it possible to generate coordinte of these missing residue?
I have a pdb file of other protein of same family in this pdb file N-terminus is random coil and turn and in my query pdb N-terminus is random coil and 3-10 helix.
I have predicted the secondary structure for missing residues they are random coil and sequence identity is of query with template except N-terminal is 68%.
So is it possible to model a protein of query sequence using above mension known pdb file?
Sangita Kachhap JRF BIC,IMTECH CHANDIGARH
On 4/25/11 11:49 PM, Sangita Kachhap wrote: > I have a pdb file and coordinate of 13 amino acid (N-terminal arm)are missing in > this pdb file. > > Is it possible to generate coordinte of these missing residue?
However, the coordinates are unlikely to be correct, since your missing residues are at the terminus. Since only one end is anchored, there's a lot of conformational space to explore. Thus, I would suggest you build a model without this terminal region.
Ben Webb, Modeller Caretaker