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The other variable was the incorporation of Xplor-NIH's refinement potentials, as described in.
Xplor-NIH's refinement potentials (the RAMA and HBDB potentials) are not intended to greatly perturb convergence of the solution.
The "refinement potentials" included the docking potentials, Xplor-NIH's RAMAchandran (backbone dihedral angle database) potential (23), and the HBDB (dynamic hydrogen bonding) potential (24).
The 10 lowest-energy structures calculated without extra refinement potentials, but with a positive charge on W7's amine nitrogen, are deposited as PDB entry 2KFX.
In the last stage of the calculation, the velocities from the previous dynamics run were inputted, and the system was equilibrated with all protein atoms reconfiguring against the refinement potentials.
Similar(55)
We suggest that rapidly growing dendrites have a pronounced effect on the grain structure of conventionally grown multicrystalline silicon, and that their unpredictable occurrence limits the grain refinement potential for the most common growth conditions.
The purpose of this study was to evaluate HOP implementation with the goal of informing HOP refinement and potential future HOP dissemination.
In addition, the use of this model can contribute substantially to the reduction, refinement and potential replacement of animal experiments (the '3R' principles).
The use of client led goal setting interventions for those with poor cognition should be approached with caution, and further refinement in potential interventions is needed for those with poor cognition.
It's not going to give someone medal potential, it's about refinement to the potential they already have".
In the past decade, progress in hardware development, improvement in simulation methodologies and refinement of interaction potentials have rendered the possibility to model increasingly complex processes that were intractable previously (Karplus and Kuriyan, 2005).
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