SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
Figure 4
SnugDock conformational diversity.
(A) The diversity in conformation generated by SnugDock during docking of anti-HEL Fab fragment (1BQL) to bobwhite quail lysozyme (1DKJ). (B) View facing the paratope. Crystal structure, red; heavy and the light chains, blue and yellow, respectively; light and heavy chain CDRs, orange and cyan, respectively; SnugDock sampled CDR H3, grey; EnsembleDock-plus-SnugDock sampled CDR H3, light chain CDRs and light chain framework, green, light orange and yellow-green, respectively. Structures are all superposed onto the heavy chain framework residues of the crystal structure. (C) Mean rmsd from the starting structure of the ten lowest-energy docking decoys for fifteen targets. For light and heavy chain CDRs, the corresponding framework chain is superposed and the rmsd is queried over the respective CDR residues. VL-VH denotes the rigid-body rmsd divergence of the heavy chain framework when the light chain framework is superposed. The paratope comprises all CDRs, and the rmsd was computed by superposing the paratope and querying over the same residues. The colors of the bar correspond to the colors of the different antibody segments in (A) and (B). The error bars denote one standard deviation.