Larger angular step sizes lead to faster computing times, but at the risk of missing the global interaction energy maximum, leading to a dependency of the spectrophore values on the actual starting orientation.
We demonstrated that the present protocol is robust to the precise starting orientation of the peptide near the binding site (Fig. 4 and Table S3).
In all MD runs, hPS preserves its starting orientation that corresponds either to the cluster M2 (in MDrand/randM2 (Figure 5E)) or cluster M1 (in randM1 (Figure 5D)) from the TOP10 set.
Participants then had to rotate the avatar back to its starting orientation to start the next trial.
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).
To promote the gameplay, participants still had to finish the trial in this case, by aligning the avatar with the egg to smash it and then returning to the starting orientation.
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.
We found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site.
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.
Without unambiguous cues to depth, the direction of this rotating walker remains ambiguous; the changing 2-D pattern can be interpreted as a walker rotating in either clockwise (CW) or counter-clockwise (CCW) directions, with the respective interpretations having opposite starting orientations relative to the observer (Figure 1B).
