Sentence examples for binding site is calculated from inspiring English sources

The enrichment of each miRNA binding site is calculated on the basis of its abundance in the EC-restricted set and the background set.

The exposure of the binding site was calculated by using the SiteMap package [41] version 3.3 (Schrödinger).

The partial charges for the ligand binding site were calculated using the MMFF94x force field and the ligand partial charges were calculated with AM1BCC charges [51, 52].

The hydrophobic and electrostatic properties of the binding site were calculated by the program Grid4.

The percentage of peaks containing at least one significant motif within 250 bp of the predicted binding site was calculated for additive 50 peak increments throughout the each program's ranked list of peaks.

The volume of a DFG-out model's binding site was calculated using POVME v2.0.

The energy for each binding site was calculated from these filament directions (see L ).

For qPCR of ChIP analysis, one primer set was used for each tested binding region (Supplementary Table S18) and ChIP efficiency of each binding site was calculated by comparison of the percentage of ChIPped DNA against input chromatin to this percentage at a negative control region.

The cavity volume at the binding sites was calculated, using DS (Binding Site module) for the coordinates obtained from protein data bank (c-Src, PDB ID: 1YOL, 1Y57, 1FMK, 2H8H and for c-Abl, PDB ID: 1M52 and 2FO0).

Binding free energies of probes that bind strongly to the RNA at the predicted binding sites and potential alternative binding sites were calculated at 4, 22, and 37 °C using the nearest neighbor model and 2′- O-methyl RNA/RNA parameters with bonuses for LNA modifications (37− 40).