Three RMSD scores were calculated based on the use of the structures. RMSDMHC is the RMSD for the structure of the MHC molecule alone, RMSDpeptide is the RMSD for the structure of peptide alone, and t
A starting alignment was built if other sequences with a known PDB structure were available, by performing a GH19 domain structure-based alignment generated through the mmaker...
Cα’s of each proteins were compared to each other using align function in PyMol. Values shown are RMSD/Cα expressed in angstroms (Å). In parentheses used vs. total number of Cαs after five cycles is s
For all the RMSD calculations, the alignments A1 and A2 were based upon the protein Cα atoms (the group of atoms G for A2 corresponds to the 80 s loop or to its three sub-regions 82–83, 84–93, and 94–
Note: C-alph (RMSD values for pairwise C-Alpha atom superposed by sequence alingments); N-loop (N-terminal loop superposed by 9 residues); β region (the first β-sheet region superposed by 7 residues);
