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Molecular docking enables the evaluation of preferred binding orientation and affinity of small molecules to their protein targets.
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Unlike the top-scored binding modes obtained from molecular docking, MD simulations enabled us to (1) analyze all the binding modes by averaging all ligand protein interactions identified in each frame of the simulation, and (2) determine the most favorable interactions.
To benefit from this concept, which has been known since 2000, it is essential to develop and improve new tools that enable molecular docking simulations of fully-flexible receptor models.
An atomic resolution crystal structure of PPIL1 in complex with the inhibitor CsA, the identification of the minimal PPIL1-binding epitope of SKIP and previously published NMR data [1] enabled us to carry out a molecular docking study.
In the future, the accuracy of Drug-EvoD can be further improved with additional features, including 3-D structural models of proteins and drug compounds, which will enable us to predict drug efficiency using molecular docking techniques.
Based on the molecular docking, dynamic studies explain binding, compare stability of the ligand protein complexes, and enable determination of interactions important in the binding modes of the ligands".
Investigation of the putative binding mode by molecular docking studies of the most active compounds ergosterol peroxide (2) and ganodermanontriol (13) enabled insight into the binding mode, which revealed crucial hydrogen bond interactions between the contemplated structure and Arg331 of the nuclear receptor backbone.
Molecular docking is a key tool in structural molecular biology.
Molecular docking studies further substantiated screening results.
Molecular docking studies have been established.
Finally, molecular docking were applied to compare experimentally determined binding parameters with molecular modelling.
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