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![[Figure 8]](nz5014fig8mag.jpg)
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Figure 8
Crystal and binding-site bottleneck radii and their relation to the minimum projection radii of molecules with a single calculated conformer. (a) The crystal bottleneck radii are plotted against the minimum projection radius of the individual soaked molecules. (b) The bottleneck radii observed in front of the small-molecule-binding site are plotted against the minimum projection radius of the molecules. The line of identity is provided to highlight false-negative results. The points are colored according to the kernel-density estimate using Gaussian kernels visualizing highly occupied regions in the data set. (c) Loop flexibility resulting in false-negative predictions with LifeSoaks as shown for the structure of human oxidized purine nucleoside triphosphate hydrolase (PDB entry 6glg). The atom and cartoon representations are colored according to their B factor and the black sphere indicates the bottleneck position. The channels predicted by LifeSoaks are depicted in yellow with a cutoff radius of 2 Å. (d) Insufficient electron-density support for bottleneck-constituting residues leading to false-negative LifeSoaks predictions, as illustrated using the structure of mevalonate diphosphate decarboxylase (PDB entry 6e2v). The electron density (2Fo − Fc) is shown as a grid at a sigma level of 1. Residues within a 5 Å environment of the bottleneck position (black sphere) are shown as sticks and their atoms are colored according to their B factor. (c) and (d) were generated with PyMOL (Schrödinger). |
![[Figure 8]](nz5014fig8.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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