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Specification of the drug binding site will result in docking around the given three-dimensional coordinate.
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They also concluded that deletion or insertion of the amplified regions or changes of nitrogenous base that alter primer binding sites will result polymorphisms in RAPD profile.
Binding of a molecule to one such site will result in hiding of the mutually exclusive binding site by sterically blocking its accessibility and thereby inhibit binding of the competing molecule.
ClusPro also uses the FFT-based rigid docking with an addition of low energy results clustering under the assumption that a native binding site will have a wide free-energy attractor with the largest number of results [ 81].
However, a protein with n binding sites will have 2 n possible states, which results in a combinatorial explosion of entities and reactions (Hlavacek et al. 2003, Blinov et al. 2004).
Simultaneously, higher TF (or binding site) concentration (activity) will result in regulation at degenerate sites (i.e. lower affinity) (see [ 1]), a conclusion that correlates well with the mechanism of control of TF-activity itself as this involves a change in affinity of the TF for the operator upon induction [ 34, 85].
NCaBD containing two Ca2+ binding sites will need to be fit with a two binding site model.
Also gross chromosomal alterations not affecting closely located primer binding sites will not be reflected.
Any perturbation of a binding site could result in a functional effect, since reducing transcription factor binding will cause deregulation of the target gene, whereas introducing a new site could cause undesired transcription (De Gobbi et al. 2006).
Inactivation of a ligand binding site can result from absence of an antibody chain, inappropriate assembly, misfolding, or unexpected modification of the binding site, and will affect the response ratios.
The presence of an SNP on a binding site can result in several different effects.
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