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Regarding molecules, we consider a molecule to be saturated when all its atoms are saturated.
Thus for simplicity, and mindful of the fact that each level represents a layer of molecules, we consider the glass to be infinitely deep in effect.
To limit clusters to a volume accessible by small molecules, we consider only clusters where the centers of mass of any two residues in the cluster are less than 12Å apart.
This approach is basically a generalization of the usual connection between the microscopic and macroscopic responses, where instead of averaging over the orientations of several molecules, we consider harmonophores and their relative orientations.
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The last molecule we considered for the detection of tumour contamination is ErbB2, a tyrosine kinase receptor of the EGF receptor family.
For each small molecule we considered QTL peaks with at least a LOD score of 2 (Table 3; see Additional file 7 for dose responses used in QTL).
All the exposed water molecules, which we consider as a part of the bulk solvent, are removed, while the buried water molecules are kept as a part of the complex.
Because we can assume that every cell contains approximately one million mRNA molecules, we can consider the values in ppm as copy numbers of the transcripts in a cell [ 27].
But there's a big gulf between "organic molecules" and what we consider today to be a living organism.
Therefore, from this set of 1 % top-ranked molecules, we only considered the molecules that were common to the four programs.
While the SPP does not provide any guidance on how to rank molecules by structural similarity, as a starting point we consider molecule A and B to be similar if it is reasonable that a medicinal chemist would synthesise and test A and B around the same time as part of the same medicinal chemistry program.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com