We performed two versions of the test: (a) we examined all bases of the predicted TF binding sites, and (b) we examined just the four most essential "core" positions of the binding region, as defined in MatBase.
Another main feature of STAP is the utility of genome-wide binding data not only as binary indicators of TF binding regions, as been done by most existing studies, but also as quantitative measurements of the binding strengths.
The central GTPase domain containing conserved nucleotide binding regions as well as switch I and switch II stretches is extended at its N- and C-terminus by further septin-specific structural elements [ 7, 8]. S. cerevisiae septins have been expressed and purified from E.coli.
The inclusion of a sequence as a bZIP 'hit' required both the presence of an LZ and a typical DNA-binding region, as defined by [ 30] and the 2ZIP program [ 31].
We note that previous bioinformatic analyses involving GPCRs have uncovered residues located in the ligand-binding region as well as within the receptor core [15], [18], [19], [77] [85], but whether all identified positions have the same statistical significance is not obvious.
Quite unexpectedly, we found that the binding of 1 completely disrupts the Zn2+ binding region, as evidenced by a total lack of electron density for residues 91 109 and the Zn2+.
We initially identified cyclin D1 as a binding partner of BARD1 in a yeast-two-hybrid screen and defined the minimal binding region as the N-terminus of BARD1.
Through MotifNetwork, we found that all 100 sequences have a glutamate binding motif, which was expected because we took glutamate binding region as our PSI-BLAST probe.
Although we were unable to obtain X-ray crystal structures for our best compounds bound to the protein, direct and competitive ITC experiments strongly implicate the FxxA binding region as the most probable binding site.
