Sentence examples for binding was calculated using from inspiring English sources
The specific binding was calculated using Biaeval 3 software (Biacore, GE Healthcare) with the postulate of 1 1 ligand/analyte interaction.
To measure the strength of interaction between the two peptides in the c-Fos c-Jun and c-Fos c-Jun c-Fos c-Junthe andolute free energy of binding was c-Jun c-Junusing the MM/GBSA method.
The chemical shift of the PHD1KDM5B backbone atoms amide 1H and 15N after H3K4me0 peptide binding was calculated using the following equation: Δ δ av = 0.5 × Δ δ ( NH) 2 + 0.2 × Δ δ 15 N 2 1 / 2. (B) Ribbon representation of free PHD1KDM5B.
The percentage of binding was calculated using the formulation: % = 100* OD450 of labeled scFvFc + unlabeled scFvFc)/(OD450 of labeled scFvFc + PBS).
The cumulative binding was calculated using equation (2) as described previously.
The percentage in vitro binding or nonspecific binding was calculated using the following equation: percentage binding=(γ after incubation/ γ before incubation) × 100.
Free energies of binding were calculated using g_mmpbsa 97, with polar solvation energies corrected by generating ion-accessibility and dielectric maps incorporating the membrane environment (dielectric slab constant is set to 2.0 using the draw_membrane2 program) through in-house python scripts98.
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).
For a given SNP V, we estimated its effect on the binding of a particular transcription factor tf, denoted by the matching score S tf (V), by evaluating the binding affinity differences between reference and alternative alleles; the binding affinity was calculated using the position weight matrices (PWMs) documented in the TRANSFAC database using previously published methods (Wang et al., 2008).
The binding energy was calculated using a scoring function London dG [49], [50],[50].
For each target peptide, the binding energy was calculated using those 99 energy matrices.
