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59% of these binding sites were supported by both replicates from control HeLa cells, and the number of crosslink events within the binding site was highly correlated between the replicates.
Among the validated sRNA target pairs, we observed that many binding sites were supported by evident degradome signatures resided within the canonical cleavage sites (10th to 11th nt of the regulating sRNAs).
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To decipher which of these three binding sites is supported by the β-catenin/LEF1 complex, reporter gene assays with constructs harboring sites for either IRF3, AP-1 or NF-кB were performed.
The functional significance of the HLS1 EIN3 binding site is supported by a previous study that identified two allelic mutations in the HLS1 promoter sufficient to yield a 'hookless' phenotype (Lehman et al., 1996).
Expanding the database of protein functional sites was supported by the RSF grant No.14-24-0123, analysis of the characteristics of structural and functional organization of the ligand-binding sites of proteins was carried out with the support of the RFBR grant No.15-04-08065, analysis of genes expression characteristics (RNA-seq data) was supported by the RSF grant No.14-14-00269 No.14-14-00269 No.14-14-00269
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Within this model, two sequential ATP-binding hydrolysis release cycles must occur; simultATP-binding hydrolysis releaseg at two independent ATP binding sites is not supported by the stricyclesyperbolic ATP dependence of kstep and kATP.
Except for the occurrence of one FTZ-F1-like binding site in the Am-C gene (GB13298; Figure 9), which is very similar (over 80%) to the consensus sequence, the presence of FTZ-F1-like binding sites was not supported by any of three enrichment scores used in our computational analysis (pipeline designed for cis-regulatory motifs discovery; Church >0.05, ROC-AUC <0.5 and Enrichment score > 0.05).
Moreover, nearly perfect matches around the 10-nt from the 5′-end of miR390 binding sites suggested that both binding sites were cleaved, which were further supported by the phased sequencing reads starting at the position of the cleavage sites of both 5′- and 3′-end target sites.
Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification.
Putative miR binding sites were listed only when their presence was also supported by an independent algorithm, miRanda [18].
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