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In designing the synthetic derivatives, we focused on the binding position of the fatty chain.
The simulations reveal a strong dependence of the conformational ensembles on type and binding position of the bound substrates and a nonsymmetric behavior of the lid domains.
This study clearly shows that the number and the binding position of the fatty chain are critical for protective activity against ER stress-dependent cell death.
The correct binding position of the ligand was obtained after the MDF stage of Shaker with an improvement of RMSD from 6.8 to 1.7 Å (Fig. 7, Additional file 3: Supporting Movie 2).
It has been reported that the binding position of the antisense RNA may determine gene-silencing mechanisms [34], [35].
Second, the HA structure was aligned against known HA-receptor complex templates and the binding position of the receptor analog in the HA receptor binding domain was initialized.
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a, Viewpoint histograms showing binding positions of the cyclization sequences along the ZIKV genome in control libraries; related to Fig. 2b.
We also found that binding positions of the receptor analogs relative to HAs are highly conserved and the backbone conformation at receptor binding region is almost fixed, when analyzing the co-crystal structures involving HAs from different type A viruses.
The ZDOCK algorithm in Discovery Studio uses the fast Fourier transform (FFT) correlation techniques and searches all possible binding positions of the two proteins.
The binding position of substrate in the active site was determined but interaction between the substrate and Ser-464 or Leu-465 was not observed, although amino acid residues at these two positions are the only structural distinctions between wheat and rye glucosidase catalytic pockets.
Additional intriguing dimensions to the recognized promiscuity of QacR-multidrug interactions are highlighted by the significantly altered binding position of Et in the QacR(E90Q -Et complE90Q -Ethe two distincomplexbinding sites found in the structure of Qand(E90Q)-R6G.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com