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algorithm python » algorithm within (Expand Search), algorithms within (Expand Search), algorithm both (Expand Search)
python function » protein function (Expand Search)
algorithm from » algorithm flow (Expand Search)
from function » from functional (Expand Search), fc function (Expand Search)
algorithm b » algorithm _ (Expand Search), algorithms _ (Expand Search)
b function » _ function (Expand Search), a function (Expand Search), i function (Expand Search)
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A) Probability density of glucuronate-UDP as a function of three collective variables (CVs): the distance between the C6 atom of the sugar and the atom of Lys307, defined as <i>d</i><sub><i>k</i></sub>, and the two angles <i>γ</i> and <i>θ</i> describing the orientation of the sugar ring in a polar coordinate system. B) RMSD of the probability density with respect to the initial state, calculated after 1 ns of simulation. The density of states is complex, and stable populations are observed at the end of the simulation. C) Probability density of glucose-UDP. D) RMSD of the density of states calculated as in B). In this case, convergence is even clearer. The density functions were computed by including all replicas from the Hamiltonian replica exchange simulation, with weights determined using the WHAM algorithm.
Published 2025“…The density functions were computed by including all replicas from the Hamiltonian replica exchange simulation, with weights determined using the WHAM algorithm.…”
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Objective function values of the algorithms across individual problem instances grouped by scale: (a) Small, (b) Medium, (c) Large, (d) Super-Large.
Published 2025“…<p>Objective function values of the algorithms across individual problem instances grouped by scale: (a) Small, (b) Medium, (c) Large, (d) Super-Large.…”
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