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Obviously, the structural differences among them are attributable to the differences of metal ions, counter anions and coordination modes of ligand.
The labile conformations and coordination modes of ligand L, which were finely tuned by reaction conditions, perhaps play the key role in the construction of various architectures.
These proteins both use Duffy-binding like (DBL) domains, a Plasmodium specific fold, to bind host carbohydrates, but recent results show that they differ significantly in their architectures and modes of ligand recognition.
NMR spectroscopy is an established tool in drug discovery, but its strength is commonly regarded to be largely confined to the early stages of hit discovery and fragment based drug design, where NMR offers unique capabilities of characterizing the binding modes of ligand molecules that bind sufficiently weakly to be in rapid exchange between bound and free state.
However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts.
A collection of modes of ligand binding by β-propellers.
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Integrating the knowledge about the binding modes of ligands in different conformational states of the protein, separate pharmacophore models were generated and used for virtual screening to explore potential novel hits.
We envision that Wrap 'n' Shake can become the tool of choice for systematic exploration of multiple binding sites and modes of ligands in drug design and structural biology.
Mapping of benzene occupancy for trajectory structures with similar benzene binding modes at the pocket correlated well with previously seen interactors of the pocket, showing that our ligand-mapping simulations reproduce crystallographic binding modes of ligands on the PBD surface.
Structural information such as that above provides detailed binding modes of ligands in their respective active sites and can be utilized to generate scaffolds with similar or improved binding affinities with novel functionalities.
Belorusova, A. Y. et al. Structural insights into the molecular mechanism of vitamin D receptor activation by lithocholic acid involving a new mode of ligand recognition.
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