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• W4200403886 abstract "Small molecules are major players of many chemical processes in diverse fields, from material science to biology. They are made by a combination of carbon and heteroatoms typically organized in system-specific structures of different complexity. This peculiarity hampers the application of standard force field parameters and their in silico study by means of atomistic simulations. Here, we combine quantum-mechanics and atomistic free-energy calculations to achieve an improved parametrization of the ligand torsion angles with respect to the state-of-the-art force fields in the paradigmatic molecular binding system benzamidine/trypsin. Funnel-Metadynamics calculations with the new parameters greatly reproduced the high-resolution crystallographic ligand binding mode and allowed a more accurate description of the binding mechanism, when the ligand might assume specific conformations to cross energy barriers. Our study impacts on future drug design investigations considering that the vast majority of marketed drugs are small-molecules." @default.
• W4200403886 created "2021-12-31" @default.
• W4200403886 creator A5005907422 @default.
• W4200403886 creator A5026034661 @default.
• W4200403886 date "2021-12-13" @default.
• W4200403886 modified "2023-09-30" @default.
• W4200403886 title "Improving Small-Molecule Force Field Parameters in Ligand Binding Studies" @default.
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• W4200403886 doi "https://doi.org/10.3389/fmolb.2021.760283" @default.
• W4200403886 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34966779" @default.
• W4200403886 hasPublicationYear "2021" @default.
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