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For every pair of accessible regions of two interacting RNAs a cost of interaction is calculated.
The interaction is calculated by the perturbation method.
Based on the derived framework particle/fluid interaction is calculated for single particles and particle packings.
A free energy surface describing the interaction is calculated using molecular dynamics simulations, and found to be inconsistent with a mechanism in which portal rotation drives DNA import.
The vehicle/track interaction is calculated in the time domain in order to be able t account directly for effects such as the discrete sleeper spacing.
The velocity field for the moving curves generated by this elastic interaction is calculated using the fast Fourier transform (FFT) method.
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The overall docking score of a chemical-protein interaction was calculated using simple energy calculations (electrostatic and van der Waals) with all default parameters used.
The interaction was calculated based on ∆accessiblity and chose the residues that have difference in solvent accessible area, when the protein interacts with the partner or not.
Dose-response curves were constructed, and the combination index (CI) for drug interaction was calculated.
The energies of interaction are calculated by Langevin dynamics and Monte Carlo simulation that are shown in Tables1,2,3,4,5, and6.
The thermodynamic properties of this interaction are calculated by LD and MC simulation methods that are shown in Tables1,2,3,4,5, and6.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com