NOTE: We have changed gears since this was first written. We are now using the Renzi-Ghersi template (ACE2 residues 19-83), which is just two alpha-helices. Talk to Dr. Norimatsu or an experienced lab member (Alec, Jianxiu, Emma) about decoy design.

We need to create protein data bank (PDB) files for designed decoys. The simplest design would include alpha-1 (residue 22-53), alpha-2 (residue 58-81), beta-3 (residue 347-352), and beta-4 (residue 355-359). The PDB file gives you the 3D coornidate of each atom and the order of amino acids. We need to rearrange these alpha helices and beta strands and renumber residues in order to express the decoy as a single protein. One idea is to order them as follows: alpha-1, beta-3, beta-4, alpha-2. The loop between alpha-1 and alpha-2 obviously need to be cut.

Please create PDB files for designed decoys and also for alignment files for Modeller.