Ligand-binding pocket of MHC class I proteins
A. Sorafenib bound in the pocket (determined by flexible docking). B. Peptide bound in the pocket (in the crystal structure). The extracellular ligand-binding groove of MHC class I proteins, taken from PDB 3BXN, is shown as green ribbon. In the ligand-binding pocket identified by iDTPnd, apolar atoms, negatively charged atoms, and positively charged atoms are shown in green, blue, and red, respectively. Peptide shown in (B) is a Cathepsin A signal sequence octapeptide.