Figure 1.

(A) Representation of the merging and splitting matrix F, calculated using all the detected pockets. The matrix F allows retrieving information on merging and splitting events. For each frame along the MD trajectory, pockets at time t are compared with pockets at time t – Δt, using the Jaccard index. In this example, at time t, the pockets 1, 2, 3, and 4 (in rows) have been detected and stored. At this point, the Jaccard index is computed with all pockets detected in the previous frame at times t – Δt, i.e., with pockets 1, 2, and 3 (in columns). Moving from t – Δt to t, this example shows that pocket 1 split into two pockets, forming the new pocket 4. Concomitantly, pockets 2 and 3 merged, forming a larger pocket that is still identified as pocket 3, according to its Jaccard index. (B) Schematic example of the conversion of the aggregate merging/splitting statistics N into an undirected network graph. In the matrix N, the off-diagonal red numbers indicate the frequency of the merging and splitting events, which is then reflected by the size of the edge connecting two pockets.