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Residues defining the binding sites were selected for site-directed mutagenesis.
The continuous stretch of amino acid sequences 26 mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31 mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds.
A total of 3 AR binding sites and 4 ER binding sites were selected for ChIP-qPCR analyses.
Eight gene promoters containing the C1 and P binding sites were selected.
Signature sites with different linker sequences between PNA binding sites were selected (Table 1).
Transcription factor binding sites were selected as statistically over-represented with a significance level of the corrected P-value < 0.1.
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The high quality protein model of correct topology and protein-ligand complex active binding sites was selected based on high confidence (C≥−1.5) and binding site (BS≥0.5) cut-off scores.
Thus, despite its sequence preference, it remains unclear exactly how ORC binding sites are selected from the many potential sequences; however, local chromatin structures and activities are probably important factors.
The interfaces that are not spliced in any isoform were assigned a score equal to the fraction of the all-isoforms test controls that remove the interface, and those having a score higher than 0.5 (i.e. those proteins whose alternative splicing selectively avoids the binding site) were selected.
From the first internal repeat, all residues with a solvent-accessible surface area greater than 20 Å (calculated using DSSP) and distal to the binding site were selected for mutation to cysteine (see Table 1).
The 48 compounds having high predicted activity values chosen from the combinatorial library were docked against the tubulin assembly targeting the α-β interfacial site of the homology based protein structure of tubulin chain B. The top two compounds showing maximum affinity for the colchicine binding site were selected.
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