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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.
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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.
Signature sites with different linker sequences between PNA binding sites were selected (Table 1).
Eight gene promoters containing the C1 and P binding sites were selected.
Potential transcription factor binding sites and miRNA binding sites were selected from all 6- and 7-bp DNA elements, respectively.
Transcription factor binding sites were selected as statistically over-represented with a significance level of the corrected P-value < 0.1.
Genes that had an index less than 0.7 and that also contained predicted TDP-43 binding sites were selected.
Interactions between mRNAs and miRNAs in binding sites were selected using Δ G/Δ G m values, allowing us to identify miRNA interactions with near perfect complementarity.
Potential target genes that contain SAFB1 binding sites were selected for further validation using qRT-PCR with TaqMan gene expression assays.
The primer binding sites were selected to ensure optimal amplification under universal conditions and lack of interaction during the ligation and PCR steps.
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