In humans, several hundred good binding sites for trivalent arsenicals were proposed to be present in each organ.
The position-specific inhibition of activity is not reflected in a similar inhibition of binding: all mutated versions of cis-elements appear to be equally good binding sites for (unknown) trans-acting factors [ 35].
The results from this classification are saved to a CSV file (the results file), which can be opened by any major spreadsheet software and can then be filtered as desired (for Good ligands, for Good binding sites or for both).
Therefore, even for a good binding site there is no guarantee that it will influence transcription of neighboring genes.
Our new MIL formulation captures the minimal constraints that a good binding site classifier needs to have, and we believe this is the reason for its better accuracy.
Nevertheless, in individual cases the improvement can be great enough to change a Dubious ligand in a Bad binding site to a Good ligand in a Good binding site (Figure 4).
Low values of P binding (g) = P E g | ε, L), indicated the presence of a good binding site.
In the case of the binding sites, the Good binding sites in the EDS account for 19%, while in PDB_REDO, they account for 36%, although only 67% of the Good binding sites in the EDS are classified as Good for PDB_REDO, and some of them are even classified as Bad.
With 55 Good ligands and 57 Good binding sites (43 of them being Good binding sites with Good ligands), there should be enough Good structures for most uses; it would not be necessary to review the Dubious ones.
What accounts for the lack of occupancy at perfectly good binding sites?
