Binding site, definition

Before docking can proceed, most docking programs require an approximate binding location to be defined. Most commercial software packages include tools for binding 

Once the binding region is selected, care should be taken with the actual definition of the binding site specified in the docking program of choice the user needs to ensure that sufficient atoms are considered to allow unbiased docking of any possible ligand of a reasonable molecular size. 

High success rates are observed for short radii. The effect is, however, misleading smaller spheres around the ligand reduce the search space and so focus 

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Self-assembled structures can be closed if all the potential binding sites are utilized, or open if they are not. Closed assemblies have a definite geometry and stoichiometry, while open assemblies exist as mixtures of oligomers or polymers of varying stoichiometry. In addition, the self-assembled structure can be classified as cooperative if the multiple binding interactions reinforce each other to yield enhanced stability, or trivial if the binding interactions do not cooperate in the... 

Classical approach, following Furchgott, and based on the early view that all the receptors occupied by an agonist are activated First, we recall one of our two earlier definitions of pAR, the proportion of binding sites occupied by A ... 

While it is reasonable to assume that kinks are formed at the site of the covalent binding of BaPDE (34), it is also possible that such bends arise elsewhere on the double helix, due to the known formation of nicks and single-strand breaks (35,36). Therefore, the existence of kinks in the DNA helix at site I or site II binding sites should be further investigated, before such a model can be adopted definitively. 

Table V. Definition of Binding Sites for Intercalation and Intercalative Covalent Binding3...

Fig. 13. Schematic illustration of metal-organic molecular squares, assembled from linear organic linkers and 90° metal units (left), linear metal units and organic comers (middle), or linear metal units and 90° metal units (113). The latter two classes have several inner-cavity binding sites and thus fit the definition of metalated container molecules.

In this chapter, it will be described how we have utilized endogenous and engineered Zn2+ binding sites to explore the structure and molecular function of Na+/Cl -depen-dent neurotransmitter transporters. The work has not only allowed the definition of the first structural constraints in the tertiary structure of this class of transporters, but also provided new insight into both conformational changes accompanying substrate translocation and mechanisms governing conformational isomerization in the translocation cycle. In the chapter, we will also review the theoretical and practical basis for... 

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