The other three interfaces form, mainly through an α-subunit, noncatalytic nucleotide-binding sites, which bind the ATP analog in the crystal.
This could be accomplished, for example, by either collecting independent experimental binding data or training the method on clusters of similar binding sites, which presumably bind the same or chemically similar ligands.
One major difference between the ChIP and the SELEX technology is that ChIP is directed towards the identification of sites that are bound in vivo under specific growth conditions, while SELEX identifies binding sites which are bound in an in vitro reaction.
In addition, the NF-κB family of transcription factors consist of five members, p65, c-REL, REL-B, p50 and p52 [ 66], and the NF-κB reporter contains four repeated, canonical NF-κB binding sites which can be bound by the different NF-κB subunits.
Given the reliance of the CRE-finding algorithm used in the present study on clustering of phylogenetically conserved Crx binding sites which contain the canonical 'TAAT' sequence bound by many homeodomain TFs, putative regulatory peaks predicted around non-photoreceptor genes must be interpreted with caution.
The distal NFAT site has been described as a "pure site," which binds NFAT in the absence of other factors, whereas the proximal NFAT binding site lies adjacent to an AP-1 binding site (42).
Many of these genes do not have canonical AHR binding sites, which raises the possibility that AHR binds to them indirectly, through protein protein interactions with other transcription factors, as is the case of AHR retinoblastoma (RB) and AHR E2F1 interactions (Ge and Elferink 1998; Marlowe et al. 2008).
Frembgen-Kesner et al. showed that cryptic drug binding sites, which appear only when the target has bound a ligand already, become more apparent over the course of MD simulations than in the original PDB structures [ 51].
Binding sites that score above this threshold will be classified as strong evidence, and binding sites, which score below, as weak evidence (Table 1).
Sum1 binds a DNA binding site which resembles, and partly overlaps, the binding site of Ndt80 [ 23], [ 18].
