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Fluid mechanical charge systems are often used for this purpose, which cause, however, undesirable sucking effects.
EEM is fast and its accuracy is comparable to the quantum mechanical charge calculation method for which it was parameterized.
Quantum mechanical charge calculations on proteins are not very common because of the highly time consuming calculation.
However, this method still limits the quantum mechanical charge calculations on the ligand and it is difficult to apply when the complex structure is not known.
Moreover, in a recent study analyzing the effect of various charge models in docking results it was concluded that the quantum mechanical charge calculation method yielded significantly better docking results [15, 18], both in terms of binding geometry and energy.
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Calculation of quantum mechanical charges using the recent linear scaling Mozyme functionality of MOPAC2009 [23] allows us to calculate quantum chemical charges on protein atoms, as well.
Specifically, we collected 18 EEM parameter sets created for 8 different quantum mechanical (QM) charge calculation schemes.
Such duplexes are cation-driven mechatronic devices, able to toggle between states with distinct mechanical and charge conduction properties.
The local mechanical and charge equilibrium equations yield a system of partial differential equations for the characteristic functions that are solved using the finite element method.
Thus, in the current study, the effect of semi-empirical quantum-mechanical partial charge calculation on docking accuracy could be investigated.
Our numerical results show that, except for the induced elastic (mechanical) displacement, charges along the dislocation loop could substantially perturb other induced fields.
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