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However, many transcriptional regulators do not bind directly to DNA and, for many that do bind, the binding site is unknown [21], [22].
When the 3D structure of the binding site is unknown, pure ligand-based approaches are often used to perceive the 3D pharmacophore.
Although the precise location of the U18666A binding site is unknown, it does not appear to be the same as the cholesterol-binding site in the luminal NTD.
The location of the weaker binding site is unknown, because only the higher-affinity binding site is occupied in the crystal structure of the SmARG NOHA complex (vide infra).
Although the existence of a dsDNA binding site on the polymerase is not unexpected, the role of the ssDNA binding site is unknown but may be required for processes involving ssDNA during replication, such as binding template DNA or ssDNA during proofreading.
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In a practical prediction situation, that size and the shape of the binding site are unknown.
Whether these sites represent transcription factors, miRNAs, or other trans-acting binding sites is unknown, but several good candidate genes are located in these regions.
The function of these potential binding sites is unknown, but suggests a role for MYF and AP-1 transcription factors in CTCF function.
For other, more species-specific dimorphic traits, the DSX binding sites are unknown but, again, the regulatory role of DSX is often antagonistic.
Users can select and use more than one cleft at the same time to perform a global search when the binding-site is unknown and interactively choose binding-site flexible side chains.
The transcription factor binding to the second site is unknown but the functionality of the site has been determined via deletion assays by Militello et al. [ 22].
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