The cover represents the docking of the Lewis Y tumor-associated antigen (tetrasaccharide) into the binding site of the antibody Fab fragment (PDB ID: 1S3K). The lowest energy pose obtained using AutoDock 3 (shown in pink) is compared to the crystallographic ligand (shown in green); with Pose RMSD = 5.7 Å for all ring atoms. Then, after the inclusion of the carbohydrate intrinsic (CHI) conformational energy, compared to the crystal ligand, Pose RMSD = 0.6 Å. The rescoring of docked oligosaccharide poses using CHI energies improves the ranking of poses generated with several docking algorithms, as demonstrated by Anita Nivedha et al. on page 526.
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