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The numbers of biotin binding sites were converted from terms of nominal concentration to terms of effective concentration of B4F by dividing by the correction factor obtained in the calibration of B4F concentration with SAv as described in Calibration of B4F Concentration.
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The correspondence between the edited sites and functional sites is summarized in Figure 2. We compared the ligand-binding residues and the residues converted by RNA editing in RuBisCO, for which binding sites for a ligand analogue are known [ 26], and found that none of the residues at the ligand-binding sites are converted by RNA editing (Fig. 1A).
A high-level description of part structures (made of, e.g., binding molecules and sites) is converted into rules that serve as inputs for BioNetGen.
Potential binding sites were elucidated by docking.
Ligand binding sites were predicted using 3DLigandSite.
Two binding sites were identified for GF.
In this case, the binding affinity of TF to TF binding sites is a proper proxy for functionality which can be converted into a probability.
As a starting point of a more detailed analysis of the evolution of prenyl converting enzymes, diphosphate binding sites are analysed.
For each binding site the alignments were converted into a post-script file and examined manually to ensure that they met the above criteria.
The appearance of beta-adrenergic binding sites was dependent on the formation of phosphatidylcholine by the enzyme that converts phosphatidyl-N-monomethylethanolamine from phosphatidylethanolamine.
Here, these binding sites are not discussed one by one.
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