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Among the 60 designed molecules 10 were selected on the basis of their binding affinity to the receptor molecule.
For every ligand-macromolecule docking a total of 10 different conformations were generated which later were analysed on the basis of their binding energy and force of attraction.
Individual aptamer sequences were screened on the basis of their binding to the 10 M-types that were used as targets.
Silicon fullerenes on the basis of their binding energies are, in fact, very stable [6 9, 40] and isolobal to the corresponding isovalent carbon fulleranes, as is indicated in Figure 10. Figure 10 An illustration of the Si and C fullerenes analogy.
The first mammalian HDACs were cloned on the basis of their binding to known small molecule inhibitors of histone deacetylation.
The result of our analysis is congruent with the three major groups of R2R3-MYBs (A, B and C) defined by Romero et al. [ 19] on the basis of their binding affinities to MYB recognition elements.
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Individual functional scAbs were ranked on the basis of their remaining binding percentage after 5 min dissociation.
The stereochemistry of the new compounds was analyzed and ligand docking experiments revealed the structural basis of their RAR binding characteristics.
Structural models of all yeast bromodomains were built using comparative modeling to provide insights into the molecular basis of their histone binding selectivity.
Thus, our assay takes advantage of the dual nature of aptamers as molecules capable of both folding into complex three-dimensional structures, which is the basis of their unique binding properties, and hybridization to specific capture probes.
Fibronectin is a modular glycoprotein (molecular mass approximately 250 kDa) that consists of a number of protease-resistant functional domains, so named on the basis of their specific binding affinity for other matrix macromolecules and members of the integrin family of matrix receptors (Fig. 1).
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