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Furthermore, we carried out docking simulation studies that could partially explain the effects of these mutations on C3′-specific hydroxylation activity.
In an effort to understand the molecular mechanism of the small molecule inhibitors binding to gp41, we have carried out docking studies, explicit solvent molecular dynamics simulations, and binding free energy calculations.
Similar to the PDB-bench dataset, we carried out docking calculations using experimental pocket centers calculated from 101 representative complex structures included in DUD-E (the D101 set).
Since the semi-empirical PM6 calculation method gives higher absolute value for partial charge on a selected atom than the empirical Gasteiger method (Figure 2), each term in the AutoDock equation was carefully considered for expected changes as a result of the semi-empirical method used for partial charge calculation before carrying out docking calculations.
To carry out docking studies, 3-D protein structures are required.
To test if this pocket could hold substrates, we carried out docking experiments using the Autodock program.
Similar(48)
As it grows, pull out dock, nettles and anything else you don't like the look of.
Diagrams and instructions are fine, but it's not until you actually "do" a lock that you really figure it out: Dock the boat, one or two jump off and open the sluices, then open the gates.
She generated income by renting out docks to commercial fishermen, and now those docks are completely gone.
Kaine snuck into an office space that was covered in ropes and boating equipment, locking the doors to keep out dock workers who were trying to get in.
Further experiments will be necessary to define the cellular and molecular mechanisms necessary to carry out DOCK-ELMO functions in the developing CNS.
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