Sentence examples for binding site predicted by from inspiring English sources
Using mutation studies of the putative binding site predicted by RNA22 we were able to confirm that the CXCL12 3' UTR is a direct target of miR-886-3p miR-886-3p miR-886-3p
To further confirm the binding site predicted by blind docking, we used Autodock v4.2.
The chemical shift changes upon H3K4me3 binding also supported the binding site predicted by structural comparison.
Then, we determined whether the sRNA binding site predicted by I NTARNA is at or close to the SD sequence.
Interestingly, the top-scoring Mg2+ binding site predicted by FEATURE corresponds to a K+ binding site in the 1HC8 structure (*1162, accuracy 1.4Å).
A double mutant containing two deletions corresponding to the miR-132-3p miR-132-3p miR-132-3pd bindingetsite (predicted2601: 5′-ACUGUUA-3′) and to a non-conserved bynding siTargetScantion 2270 (5′-ACUGUUA-3′) was less respositionto miR-132601 (p < 0.01, ANOVA corrected by BH procedure) (Fig 8A).
All the specified targets contain miR-34c binding sites predicted by at least three target prediction programs (Miranda (Enright et al, 2003), miRtarget2 (Wang and El Naqa, 2008), Pictar (Krek et al, 2005), Pita (Kertesz et al, 2007), RNAhybrid (Rehmsmeier et al, 2004), and TargetScan (Lewis et al, 2005)).
We observe that the prediction from the pattern-based method are complementary to the prediction from Ligsite CSC, i.e., for some proteins the binding sites predicted by Ligsite CSC are relatively far away from the actual binding sites while our method provides correct predictions.
The results obtained for experimental pockets (black crosses) are compared to binding sites predicted by eFindSite (blue triangles).
This improved performance of Vina holds for binding sites predicted by eFindSite as well, where using the optimized docking protocol improves RMSD by 2.5 Å and increases the fraction of binding residues and specific contacts by 10 % on average.
