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The results of Molecular docking simulations determine a general binding mode of ligand.
This mode of ligand recognition is strikingly similar to polyproline interaction with SH3 domains.
Here, we report a unique binding specificity and mode of ligand binding for a family 32 CBM.
RMSD value was calculated between the experimental binding mode of ligand rilpivirine as in X-ray co-crystallized pose in 3MEE and Glide re-docked pose to ensure accuracy and reliability of the docking procedure.
Extensive mutational and photo-affinity crosslinking studies, as well as more recent X-crystallography approaches, have revealed a common "two-site" mode of ligand binding used by each of these family B receptors.
The uniqueness of this mode of ligand recognition is corroborated by the crystal structure of TTR in complex with the weak analogue 1,5-AmNS, the binding of which is driven mainly by hydrophobic partition and one electrostatic interaction between the sulfonate group and the Lys15.
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Desensitization is an important mode of ligand-gated Ca2+ channels at synapses in the animal nervous system (Jones and Westbrook 1996).
Previous structural studies performed by us demonstrated that MjTX-II, a PLA2-like toxin isolated from Bothrops moojeni, presents a different mode of ligand-interaction caused by natural amino acid substitutions and an insertion.
Based on three-dimensional structures of complexes between ligand-binding domain of human estrogen receptor-α and its ligands, we designed mutant receptors with modified mode of ligand-binding.
The coordination mode of ligands to lanthanide ions was determined by IR spectroscopy (Fig. 2).
Docking programs are used primarily to predict the binding mode of ligands to receptors.
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