The Clover score estimates the degree of over-representation of a given sequence by estimating the thermodynamic binding energy of a transcription factor to the promoter sequences of genes in a given cluster and comparing this to the binding energy of the transcription factor to a control sequence (in this study, the 2000 bp region upstream of all mouse gene promoters).
Virtual screening approaches, historically divided into ligand- and structure-based algorithms, prioritize drug candidates by estimating the probability of binding to the target receptor [3].
By fitting the experimental data with mathematical models, the modes of interaction of LVF CTAB combinational system were quantified by estimating the partition coefficient (Kx), the binding capacities (Kb), Stern-Volmer quenching constant (Ksv) and related Gibbs free energies.
We considered the possibility that inaccuracies in our assembly of the underlying mouse genomes may contribute to the observed TF binding differences by estimating the maximum possible contribution this could make to our data.
We also investigated whether SYBR Green I dye binding is sequence specific by estimating the number of PCR product molecules at threshold using the ABI PRISM 7000 Sequence Detection System (Applied Biosystems) [ 35, 36].
We estimated the binding activity of oligonucleotides by incubating the same amounts of nuclear protein and various oligonucleotides.
The binding capability that reflects the selectivity of these diazacrown ethers to metallic ions is estimated by the binding energy.
Next, a prioritization method was applied to decide which route candidates are preferred by estimating five priority factors: binding site covalence, chemical similarity, thermodynamic favorability, pathway distance, and organism specificity.
(B) The immunoreactivity of 125I-labeled B-B4 mAb was estimated by measuring the binding of a constant concentration of 125I-labeled B-B4 mAb to increasing numbers of U266 multiple myeloma cells that strongly expressed the CD138 antigen.
