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This is because if the size difference between the dopant atoms and Mo are larger, the dopants will be bonded closer and stronger to Mo and the more negative binding energies subsequently cause the lower formation energies.
More negative binding energies indicate more stable complexes.
The more negative binding energy calculated for the least potent analog 4 probably results from a stable analog 4 Na+/K+ ATPase complex (possibly resulting from some hydrophobic and H-bonding interactions discussed earlier), but the orientation of analog 4 to the ion permeation path might not be as effective in blocking ion permeation as that of ouabain.
Our free energy calculations agree with this observation, suggesting that for this value of ε binding is very weak: K d = 0.33 M and g cc = − 1.1 k B T. Note that formation of additional bonds in a capsid structure will give rise to substantially more negative binding free energies.
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For all complexes, a more negative intrinsic binding energy produces a more stable complex and, therefore, a larger decomplexation barrier.
Because there are many more negative examples (non-binding sites) in the data than positive examples (binding site residue cluster or pocket) it was necessary to randomly select only a subset of the negative data to obtain a balanced dataset.
A more negative value indicates tighter binding.
According to their effects and the binding sites on Nav channels: i) α-class scorpion toxins for Nav bind to channel receptor site 3 and show an effect in the inactivation mechanism of the channels [ 26, 27]; ii) Scorpion β-class toxins modify the Nav activation process by shifting activation to more negative membrane potentials after binding to site 4 [ 27- 29].
More negative values mean that the binding site is less accessible for siRNA binding.
Phosphate ions binding to the Zr-hydroxide will render the average surface charge more negative, which could lead to Cd binding to the hydroxide.
More negative the docking score stronger the binding, further the desolvation energy also enables to draw correlation that greater the binding affinity more loss of water is seen at the interface.
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