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The involvement in the fusion or docking processes of homotypic SNARE clusters, built by syntaxin 1 (Sieber et al, 2007), SNAP-25 (Halemani et al, 2010) or even synaptobrevin (Bethani et al, 2009) is unclear.
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Now, biochemist Brent Iverson and protein engineer George Georgiou of the University of Texas, Austin, have created a new type of antibodies that specifically interrupt the docking process of PA.
Feasibility of the cross-linking reaction of o-NAD with Hb was assessed by studying the docking process of o-NAD within the 2,3-DPG pocket of Hb.
The hardware-in-the-loop (HIL) simulator is an important equipment to test the performance of the docking mechanisms (DMs) in the docking process of two spacecrafts on the ground.
It is noteworthy that in the boomerang cells induced by actin4 RNAi, the exocytotic capacity is reduced to 10%, showing the role of this actin4 in the docking process of the trichocysts to the membrane.
This development enables the docking process to be quantified in terms of the number and identities of the pharmacophoric hypotheses that can be matched by a compound or a library of compounds.
We previously parallelized the calculation of each docking processes using MPI and OpenMP with the master/worker model (Matsuzaki et al., 2013).
MEGADOCK has already been parallelized using MPI and OpenMP for multiple combinations of protein pairs [ 16, 17]. Figure 1 shows the flow of the docking processes in MEGADOCK, where the flow is based mainly on the Katchalski-Katzir algorithm.
Using Glide software (see Methods), the candidate ligands were docked to each of the three boxes (~1.5 million docking processes).
The inverse triangle shows that with progress in the overall docking process, the number of feasible binding poses of a ligand will be reduced.
The use of decoy sets provides a useful measure of the discriminatory power of a docking process, measuring the ability of the docking procedure to identify active compounds early from an unbiased series.
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