Likewise, we know that the GAL3 promoter has a single binding site, so we assume that two sites in GAL1/3 were lost without any additional intervening binding site gains or losses.
In fitting all three data sets, a single binding site was assumed on VCA.
The dissociation of stable complex between transcription factor and binding site was assumed to be slow and was modelled by a stochastic transition with a relative rate of 10/a.u.u
In TRANSMODIS, gene expressions are modeled by a two-component Gaussian mixture model and the binding site sequences are assumed to be generated from a multinomial distribution which is represented by a position specific weight matrix (PSWM).
The binding of the first guest acts as a stimulus, which instructs the second binding site to assume a specific size.
This indicates that the conformational effect is induced by copper binding to the transmembrane copper binding site (TMBS), assuming that the TMBS is the only residual copper binding site in ΔNMBD.
The proportionality factor between the protein-bound concentration and the concentration of the respective low-molecular-weight species is derived in a similar way, using the association constant K ijkl for the binding to the lth binding site, and assuming linear binding (i.e., a negligible loss of the binding site concentration on binding).
SNPs with high conservation scores, high positive selection scores, or within microRNAs' target binding sites are assumed to have higher disease risk [8], [9], [10], [11].
The most commonly used method is a log-odds approach in which the frequencies of bases in the binding sites are assumed to be proportional to their contributions to binding affinity [9], [22].
