Since the binding specificity of several TFs is already known, the motifs discovered can be then compared to already known motifs with tools like STAMP [ 15] or TOMTOM [ 16].
Recently, several high-throughput techniques, such as protein microarray, phage display and SPOT synthesis, have been developed, which can detect the binding specificity of various modular domains.
Relatively little is known about signaling and binding specificities of different Wnt and Frizzled proteins.
A central question is how the HOM proteins achieve their developmental specificity despite the very similar DNA binding specificities of isolated HOM proteins in vitro.
To verify the binding specificity of the identified aptamers, several methods were applied.
To determine binding specificity of PDZ-peptide interactions, several high-throughput techniques (e.g. protein microarray screening, phage display etc).
The binding specificity of 9a was demonstrated using several representative sugar phosphate phosphatases from the HAD enzyme superfamily, the T6PP protein fold family of origin.
Of particular interest were PWMs representing the DNA binding specificity of NRs that were recovered in several clusters, namely clusters 5 (VRGKTYAWTGAMMYY-Ecdysone), 6 (YGTCAWTGAC, closely related to ecdysone Receptors (EcRs) matrices) and 12 (M00526-V-GCNF_01, binding specificity of the vertebrate NR GCNF).
Fig. 2 Synthesis and chemical structures of several peptide conjugates and binding specificity of LXY30 to U-87MG cells.
Furthermore PP2A1 binding specificity of DPT-Vpr1, a peptide containing the site 1 sequence, was substantiated by testing several peptides modified by residue substitution.
