We found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site.
If the number of transects, the starting orientation, the numbers of points on each transect and their proportionate distances along the transect are all held constant then there is a point-to-point correspondence across the breasts within and between individual patients.
For all test cases, the result of wICP refinement converges to the native orientation even if the starting orientation differs by an angle of ∼50○ (Supplementary Figure S3).
The same stimulation paradigm was also used in 3 additional control experiments to examine the effects of rotation direction, starting orientations in each pair of orthogonal conditions, and stimulus presentation period.
As initial configurations, CNT and drug were aligned along the nanotube axis and separated sufficiently far away (>3 nm) to minimize the effect of starting orientations.
It should be emphasized that the biased population orientation selectivity observed here did not depend on the starting orientations in the pair of orthogonal conditions (see Supplementary Figs S1 C, D ).
For each system, five independent trajectories were obtained by starting from different orientation of the WW domain and different random velocity.
