Fig. 4: Initial pose selection strategy in first-round design. | Communications Biology

Fig. 4: Initial pose selection strategy in first-round design.

From: Targeting Ras-binding domain of ELMO1 by computational nanobody design

Fig. 4: Initial pose selection strategy in first-round design.

a Comparison of initial poses of nanobody (green) binding to ELMO1-RBD (cyan) generated by the default antibody-antigen (AA) mode and the optimized AA mode of PatchDock. Arrows (red) are approximately in parallel to the beta-strands of framework and are pointing towards the CDR loops. b Illustration of initial poses generated from the optimized AA mode in PatchDock with respect to their range of PatchDock complementarity scores among all compatible initial poses. c Comparison of the relatively less funnel-like and relatively more funnel-like binding energy landscape sampled by RosettaDock.

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