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Dry dock, type of dock (q.v). consisting of a rectangular basin dug into the shore of a body of water and provided with a removable enclosure wall or gate on the side toward the water, used for major repairs and overhaul of vessels.
Dry dock, type of dock consisting of a rectangular basin dug into the shore of a body of water and provided with a removable enclosure wall or gate on the side toward the water, used for major repairs and overhaul of vessels.
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We call their docking type "edge-to-edge".
The complex structures of 1D4V(3), 1EM8 5), and 2HSN(18) are "point-to-point" docking type.
Naturally, a shape complementarity search has difficulty in dealing with the "edge-to-edge" docking type.
In addition, the docking type of 1F2T 6) or 1Y96(15) is different from the typical type as mentioned above.
This docking type has a smaller contact surface area than the "edge-to-edge" type as shown in Figure 7(c).
The common feature of those complex structures is that, except for 1F2T 6) and 1Y96(15), they have a typical docking type that we called "surface-to-surface".
Because the docking type of 1AY7 0), 1CAU 2), 1EAY(4), 1WHM 12), 1WRD 13), 1XG2(14), and 2F9Z(16) is "edge-to-edge", the affinity scores S affinity are low (ie, under 7.54σ) for almost all the ligands.
Most of the protein pairs that our AEP system failed to predict were not the typical docking type (ie, surface-to-surface) with a complex formation as mentioned above but edge-to-edge and/or point-to-point type, because the shape complementarity search cannot deal easily with these types.
Even the affinity evaluation was derived from a shape complementarity search, because in practice, the affinity analysis revealed that a shape complementarity search can identify a pair with such a docking type in a sophisticated manner from 400 protein pair candidates.
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