Sentence examples for binding in these simulations from inspiring English sources
This stabilization leads to increased VEGFR2 complexes and resulting increased total retention of VEGF found with Model 2, as the increase VEGFR2 binding is greater than the loss of VEGFR1 binding in these simulations.
To further investigate the efficacy of our approach in analyzing repositioning time courses, we conducted an additional set of simulations in which we generated different fractions of bound ISWI by varying the probability of binding in the simulation.
Although the binding of Mnt to DNA is not strictly additive [32], in these simulations we assume that the binding energy to any sequence is the sum of the energy values from the matrix that corresponds to that sequence.
To retain the same probability of GCN4 reinitiation in these simulations, the ternary complex binding rate was also lowered three-fold.
Although using a single Gltph monomer immersed in water represents a drawback in these simulations, the results indicated that binding of Na1 stabilizes the open conformation, which is consistent with its facilitatory role in substrate binding.
The conformers of Nup153FGPxFG that were subjected to ImportinβN binding in the MD simulations were also devoid of large-scale conformational changes, and interactions were only observed between individual surface exposed residues of Nup153FGPxFG and ImportinβN.
In these simulations, the r.m.s.
The inhibitor binding site identified in these docking simulations and importantly the mode of binding, builds on the previous knowledge we have concerning the location at which these compounds act, which is currently limited.
Several experimentally testable hypotheses about the substrate binding site emerged from these simulations.
Metadynamics simulations on V2R and its V1aR-analog give an excellent correlation with experimental binding free energies by assuming that the most stable binding site in the simulations corresponds to the experimentally determined binding free energy in each case.
In all these simulations, an acceptable residual risk was sustained.
