LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments

Pletzer-Zelgert, J.; Ehrt, C.; Fender, I.; Griewel, A.; Flachsenberg, F.; Klebe, G.; Rarey, M.

doi:10.1107/S205979832300582X

Figure 4
A two-dimensional schematic of the LifeSoaks algorithm. The unit cell includes two internal vertices, four surface vertices, five internal edges and two artificial surface-connecting edges marked *. We note that $[r(e_{1}) = r(e^{\prime}_{1}) = r(e^{*}_{1})]$ and $[r(e_{2}) = r(e^{\prime}_{2}) = r(e^{*}_{2})]$ due to internal point symmetry. Further, r(e₁) > r(e₂) > r(e₃). (a) The state before any edge is processed. In this iteration the bottleneck radii are determined from left to right, so vertices on these sides are marked as surface vertices (magenta coloring) and e^*₁ is excluded. (b) After two iterations e₁ and $[e^{\prime}_{1}]$ have been processed, since they are the largest edges. Because they connect one new vertex to a surface vertex, their incident vertex is now also accessible by one surface but not by both. (c) After three additional iterations e₂, $[e^{\prime}_{2}]$ and e^*₂ have been processed. Since e^*₂ connects the surface vertices at the top and bottom, all vertices are now part of the same set. Since this set now contains vertices of the opposing surfaces, it represents a unit-cell-traversing path and all vertices will be annotated with the bottleneck radius r(e₂). (d) Finally, e₃ is processed. However, because the incident vertices are already part of the same set, no set or radius is changed.

STRUCTURAL
BIOLOGY

ISSN: 2059-7983

Volume 79| Part 9| September 2023| Pages 837-856

https://doi.org/10.1107/S205979832300582X

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