The TFBS duplex stability scores are computed for all the binding sites of a promoter sequence.
Fig. 5 Heat map showing clustering of SiteHopper PatchScores within proteins of the same target class for potential binding sites of a HIV-1 Protease, and b prothrombin.
Remarkably, Geomfinder detected identical 3D patterns associated to the binding sites of a common substrate in two fylogenetically distant proteins such as SERT and MAO-A.
SiteMap characterizes the possible binding sites of a protein by analyzing several physical chemical properties, such as size, volume, exposure to solvent, hydrophobic and hydrophilic space, and H-donor/-acceptor ability [43, 44].
Furthermore, applying the CSI binding data to genomic sequence (genomescapes) provides a powerful tool for identification of potential in vivo binding sites of a given DNA ligand, and can provide insight into differential regulation of gene networks.
During evolution, eukaryotic PFK1 enzymes developed by duplication, tandem fusion and divergence of catalytic and effector binding sites of a prokaryotic ancestor [12].
GITTAR is a probabilistic model that incorporates sequence motif and ChIP-chip ratio to identify the most reliable binding sites of a TF of interest.
By sf,g we denote the number of binding sites of a transcription factor f∈GF predicted within the DNA sequence around a gene g∈GA.
For a given double graph of interactions, the number of binding sites of a gene is determined by the number of edges that end up in the corresponding graph node.
This model may be applied to a system in which a molecule exhibits two distinct binding states involved in the interaction with the free binding sites of a partner molecule to form a complex.
By promoter analysis, we identified binding sites of a set of transcription factors, including FOX, GATA, MYB, NANOG, OCT, PAX, SOX and STAT, as well the FGF response element, which may represent key regulatory mechanisms underlying the conserved co-expression in the ESC-critical pathways.
