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Besides, Surflex-dock is employed to explore binding mode of the inhibitors studied when acting with BACE-1 enzyme.
Finally, molecular modelling and simulation were used to explore binding characteristics of 5-oxo-ETE and derivatives with the aim to rationalize biological activity.
To explore binding within the Phe43 cavity, we first examined region 1 congeners.
Unrestrained molecular dynamics simulations explore binding conformations close to each other, hence the docking poses obtained were clustered by root mean square deviation (RMSD) in order to avoid selecting conformations that interconvert during the simulations time scales.
To aid in this understanding and further explore binding partners of these proteins, we performed an unbiased proteomic approach using HaloTag technology as previously described (Los et al, 2008; Daniels et al, 2012).
In summary, results of our work widen the knowledge of interactions between transcription factors and their binding sites, which will help us further investigate transcriptional regulation and explore binding mechanisms between proteins and DNAs.
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Biochemical investigations exploring binding properties of WSP are currently ongoing and will help elucidating the role of WSP in the invertebrate hosts.
To explore carbohydrate binding further, the binding kinetics was determined for yeast invertase, mannan and gp120 from HIV that all possess high-mannose oligosaccharides.
The research involved virtual screening of 37 different molecules by molecular docking studies performed by Molecular Design Suite (MDS) into the ligand binding domain of PPAR-γ receptor to explore the binding affinity and conformations of the molecules.
To further explore the binding of MTα to the α2B-adrenoceptor, we performed ligand binding experiments on Sf9 cell homogenates with [3H]RX821002 as reporter ligand.
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.
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