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Based on key residues information, the model of HWTX-XI was docking to fit the surface of the pocket region of KV1.1 manually for KV1.1/toxin complex construction (Methods S4).
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Each peptide library was docked to the ETS monomer conformations obtained from the clustering.
In addition, a partial GDH structure was docked to the Sirt4-NAD+ complex model.
A library of ∼12,000 small fragments was docked to explore the area surrounding the zinc ion.
A database of over 200,000 compounds was docked to the active site of AmpC β-lactamase to identify potential inhibitors.
The native pentapeptide with the sequence Alanine-Arginine-Serine-Alanine-Arginine was docked to the enzymatic subunit.
The glucose was docked to the QLS site and ATP was docked to the ATP binding site (Figure 1A).
ATP molecule was docked to DDX3X structure and the structure was energy minimized.
This map was docked to the EM map of GroES-ATP7- single-ring GroEL GroES-ATP7- single-ring GroEL
As a negative control, celebrex, another unrelated drug, was docked to the same collection of pockets.
Glucose was docked to the glucose transportation pore and ATP was docked near the ATP binding motif located at the loop between TM8 and TM9 (Figure 1A).
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