Peptide – human class II MHC docking results.

Self-docking results are indicated by asterisks. The PDB ID for the MHC structure used in docking is shown in parentheses for each allotype. All-atom RMSDs were calculated for all non-hydrogen atoms in the peptide residues that contact the MHC in the experimental structure. The core RMSDs include only peptide residues P1–P9 (underlined in the peptide sequence) whereas the other values include all simulated residues from P-1 to P10. The highest resolution MHC structure, in parentheses, was used for each allotype. The RMSD values were calculated after aligning the MHC structures. Consecutive residue numbers in the last column are denoted by a numeric range.