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In total 50 binding modes were obtained for deltamethrin, PBAlc, PBAld and PBA.
CHK2 crystal structures (PDB ID: 2CN5 and 2W0J) representing different ligand binding modes were obtained from the Protein databank.
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Overall, about 21.100 modes were obtained on glucose and ammonium.
The probable mechanisms and the proposed binding modes were discussed.
These binding modes were subsequently confirmed by X-ray crystallography.
Ligand binding modes were analyzed using LigandScout 3 software (www.inteligand.com).
To ensure that all possible binding modes were explored, early termination of the docking run as a consequence of multiple solutions with the same binding mode was disabled.
From a combined analysis of both data, the equilibrium constant and hence standard free energy change associated with each binding mode can be obtained unequivocally.
We designed a procedure through which information on the binding mode can be obtained using FTS.
To complement the results obtained by the molecular docking study, an in-depth investigation into the binding modes was conducted with the molecular dynamics (MD) simulation to explore the binding profile and energy landscape.
Although the low energy binding modes are prevalent no significant clustering was observed again suggesting no specificity in binding.
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