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Figure 5 | Immunome Research

Figure 5

From: pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes

Figure 5

Structural comparison between the native conformation and the lowest energy docked conformation of the cognate peptide in MHC-I complex 1duz. The peptide is shown in stick representation wherein the native conformation is in pink and the docked conformation is in blue. The MHC peptide binding ‘groove’ is shown as ribbons. The Cα RMSD between the native and the lowest energy docked conformation of the bound peptide from our work is 0.33 Å which is up to three and a half times better than an earlier reported Cα RMSD of 3.01 Å [37]. The peptide residues of our lowest energy docked conformation that were better modeled and aligned to that of its native conformation when compared to the lowest energy docked conformation reported earlier [37] are labeled in black. This structure is not listed in Additional File 1 - Table S1 since it was a redundant structure in MPID-T2.

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