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Similarly, changes in the vanadium hyperfine coupling constant with ligand binding have been calculated using model complexes and DFT methods.
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Given that many inhibitors have been studied and for many of them binding affinity constants have been calculated, it is beneficial to analyze the chemical landscape of these families of inhibitors and correlate these inhibition constants with molecular structure descriptors.
Absolute binding free energies have been calculated with alchemical methods for a few protein ligand systems.
The amino acid contributions to the free energy of binding of BH3 peptides to Bcl-xL have been calculated using molecular dynamics simulations coupled with the molecular mechanics/Poisson Boltzmann surface area method [ 12].
The binding constants of FBTC towards fluoride and copper ions have been calculated using the Benesi-Hildebrand equation, and FBTC has more binding affinity towards copper ion than fluoride ion.
Equilibrium distances, binding energies, harmonic vibrational frequencies and local charges have been calculated.
Both Kd values have been calculated assuming a standard single-site binding model (see Materials and Methods).
From the second binding event a binding affinity has been calculated, with a Kd of 0.6 µM.
Furthermore, the binding free energy has been calculated by the molecular mechanics [MM] with Poisson-Boltzmann [PB] and surface area solvation (MM/PBSA) method by using the g_mmpbsa tool.
KIR3DL1 binding free energy has been calculated as the difference between KIR3DL1-HLA-B-peptide complex and the sum of HLA-peptide complex and KIR3DL1 alone as previously reported [ 22].
The binding free energy (Δ G) has been calculated as the sum of the interactive and solvation energies.
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