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Importantly, this definition excludes potential binding sites that have not been demonstrated to bind ligands (so called unliganded binding sites), thereby creating a bias towards currently exemplified protein ligand complexes.
The principle underlying this mechanism would be similar to the use of transcription-factor binding sites that have low or modest affinity at enhancers to achieve specificity of gene expression14.
In this process, small-molecule ligand binding sites that have similar three-dimensional amino-acid arrangements are superimposed.
In summary, we show that SiteHopper is able to identify structural similarity between potential binding sites that have been detected objectively from protein structure coordinates.
This site is one of two functional Sp1 binding sites that have been characterized in the human TNF promoter [3].
All five genes have identified Ey binding sites that have been validated through in vitro binding studies and in vivo reporter assays.
Similar(29)
Cerato-platanin domain-containing proteins such as EPL (eliciting plant response-like), Snodprot, swollenins and expansins have a double ψβ-barrel fold and a carbohydrate binding site that have been shown to induce plant defense response [ 55, 56].
The promoter regions of miR-34b/34c miR-34b/34cpotential p53-bindingeneses thavehave been expotentiallly verified, and both miRNAs are part of the p53 tumor suppresitesnethatk [ 20].
Hsp90 chaperones contain an N-terminal ATP binding site that has been effectively targeted by competitive inhibitors.
The sigma-1 receptor is a unique non-opioid, non-PCP binding site that has been implicated in many different pathophysiological conditions including psychosis, drug addiction, retinal degeneration and cancer.
The peak in this track is a functional Gli3 binding site that has been experimentally verified.
More suggestions(18)
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