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This approach is especially useful when no previous peptide binding data are available.
In contrast to CTCF, no genome-wide binding data are available for the thyroid hormone receptor.
It also shows the limitations if binding data are available only for a restricted set of cell types and conditions.
They constructed a homology model of human P-gp (using the mouse P-gp as template) and successfully docked the Rhodamine B molecule, a P-gp substrate for which the experimental binding data are available.
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53 protein-ligand complexes were analyzed for which both crystallographic structure determination and binding data were available.
It is difficult to distinguish different mechanisms of cooperative interactions when only DNA binding data is available.
The particular allotypes used for testing were chosen for two reasons: (1) adequate peptide binding data was available for evaluating the prediction results and (2) they have very different peptide binding specificities so that the results reflect the generality of the prediction method for multiple MHC allotypes.
For AP1, ChIP-Seq binding data were available for all three classes (not cancer, MET, and Non-MET cancers), for both FOS and JUN TFs.
It is quite possible that, as more high-quality binding data is available, mapping some of the small differences that were inconsequential for the present analysis might subsequently turn out to be statistically significant.
More generally, the novel approach described here could be used for any cross-regulatory group of TFs for which sufficient dynamic binding and expression data are available, in order to predict regulatory logic and move stepwise toward the construction of larger transcriptional networks.
Protein binding microarray (PBM) data are available for 168 mouse HD proteins, but 14 of these (Dbx1, Hoxb5, Hoxb6, Hoxc6, Irx5, Lhx5, Lhx9, Lmx1b, Obox2, Pax6, Phox2a, Six6, Titf1, Tlx2) were removed from the dataset because their scaled BEEML-PBM PWMs (position weight matrices; see below) had a total information content (IC) <3 std below the mean IC for the entire combined set of motifs.
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