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A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach

Abstract : The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein–protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings
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https://hal.univ-lorraine.fr/hal-03114658
Contributor : Alessandro Genoni <>
Submitted on : Tuesday, January 19, 2021 - 10:23:33 AM
Last modification on : Monday, May 17, 2021 - 2:52:20 PM
Long-term archiving on: : Tuesday, April 20, 2021 - 6:41:33 PM

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Erna Wieduwilt, Jean-Charles Boisson, Giancarlo Terraneo, Eric Hénon, Alessandro Genoni. A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. Journal of Chemical Information and Modeling, American Chemical Society, 2021, 61 (2), pp.795-809. ⟨10.1021/acs.jcim.0c01188⟩. ⟨hal-03114658⟩

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