Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena

Rizzuti, Bruno

doi:10.1016/j.bbapap.2022.140757

Cited by 21 publications

(12 citation statements)

References 201 publications

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“…The small molecule Topol was obtained by fitting the bond and angle parameters based on the Hessian matrix using Sobtop [ 33 ]. Molecular dynamics (MD) simulations were used to explain conformational changes in the complex ligand–receptor binding interactions and stability [ 34 ]. All MD simulations in the current work used the GROMACS 19.5 package ( (accessed on 20 August 2022)) [ 35 ].…”

Section: Methodsmentioning

confidence: 99%

Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

Yang

Pan

et al. 2022

Foods

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Postprandial hyperglycemia can be reduced by inhibiting α-glucosidase activity. Common α-glucosidase inhibitors such as acarbose may have various side effects. Therefore, it is important to find natural products that are non-toxic and have high α-glucosidase-inhibitory activity. In the present study, a comprehensive computational analysis of 27 dietary flavonoid compounds with α-glucosidase-inhibitory activity was performed. These included flavonoids, flavanones, isoflavonoids, dihydrochalcone, flavan-3-ols, and anthocyanins. Firstly, molecular fingerprint similarity clustering analysis was performed on the target molecules. Secondly, multiple linear regression quantitative structure–activity relationship (MLR-QSAR) models of dietary flavonoids (2D descriptors and 3D descriptors optimized), with R2 of 0.927 and 0.934, respectively, were constructed using genetic algorithms. Finally, the MolNatSim tool based on the COCONUT database was used to match the similarity of each flavonoid in this study, and to sequentially perform molecular enrichment, similarity screening, and QSAR prediction. After screening, five kinds of natural product molecule (2-(3,5-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one, norartocarpetin, 2-(2,5-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one, 2-(3,4-dihydroxyphenyl)-5-hydroxy-4H-chromen-4-one, and morelosin) were finally obtained. Their IC50pre values were 8.977, 31.949, 78.566, 87.87, and 94.136 µM, respectively. Pharmacokinetic predictions evaluated the properties of the new natural products, such as bioavailability and toxicity. Molecular docking analysis revealed the interaction of candidate novel natural flavonoid compounds with the amino acid residues of α-glucosidase. Molecular dynamics (MD) simulations and molecular mechanics/generalized Born surface area (MMGBSA) further validated the stability of these novel natural compounds bound to α-glucosidase. The present findings may provide new directions in the search for novel natural α-glucosidase inhibitors.

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Section: Methodsmentioning

confidence: 99%

Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

Yang

Pan

et al. 2022

Foods

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“…In the majority of cases, researchers utilise LAMMPS because it is the simplest and most efficient technique to model particle dynamics. It is regarded as one of the oldest problems in bioinformatics, especially in the prediction of structure [29]. For this reason, LAMMPS is known as a stand-alone application because of its usage of single-scale components in a multi-scale model, which makes it stand out as a standalone application.…”

Section: Simulation Using Lammpsmentioning

confidence: 99%

A review on mechanical and material characterisation through molecular dynamics using large-scale atomic/molecular massively parallel simulator (LAMMPS)

Gowthaman¹

2023

Funct. Compos. Struct.

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Molecular dynamics (MD) simulation continues to be one of the most advanced tools in a wide range of fields and applications. The motion of atoms or molecules at various temperatures and pressures was analysed and visualised using the MD simulation through large-scale atomic/molecular massively parallel simulator (LAMMPS). This research focuses on a basic introduction to MD, as well as their determination and MD methods. LAMMPS works with a variety of external packages to determine the position of atoms and molecules over time. As the simulation has various procedures such as algorithm to step processing and results, the developers of MD are constantly pushing for the reduction of pre-steps. This classifies the performance competence that should be approached for increased portability of performance on a programmatic level, a key to implementing the solution for various problems that would come from inventors and possibly new research in programming languages.

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“…It is routine nowadays to read papers reporting simulations of complex molecular mixtures, involving mixtures of aqueous and organic solvents, together with ions, co-ions, and with much larger molecules, such as enzymes, and in the perspective of simulating realistic liquids, such as those involved in biological or pharmaceutical systems. , The recent interest in the structure of the solvation shell of hyaluronan oligosaccharides in aqueous organic solvent mixtures is among such modern simulation topics. − On the opposite side of the spectrum in terms of complexity, there are still studies of liquids such as alcohols or binary aqueous mixtures, with a particular focus on their microstructure. The computer simulations of these latter systems reveal appreciable model dependence, which often focuses on minute studies in molecular details.…”

Section: Introductionmentioning

confidence: 99%

Concentration Fluctuation/Microheterogeneity Duality Illustrated with Aqueous 1,4-Dioxane Mixtures

Kolaříková,

Perera

2024

J. Chem. Theory Comput.

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The structural properties of aqueous 1-4 dioxane mixtures are studied by computer simulations of different water and dioxane force field models, from the perspective of illustrating the link between structural properties at the molecular level and measurable properties such as radiation scattering intensities and Kirkwood−Buff integrals (KBIs). A strategy to consistently correct the KBI obtained from simulations is proposed, which allows us to obtain the genuine KBI corresponding to a given pair of molecular species, in the entire concentration range, and without necessitating excessively large system sizes. The application of this method to the aqueous dioxane mixtures, with an all-atom CHARMM dioxane model and 2 water models, namely, SPC/E and TIP3P, allows one to understand the differences in the structure of the corresponding mixtures at the molecular level, particularly concerning the role of the water aggregates and its model dependence. This study allows us to characterize the dual role played by the concentration fluctuations and the domain segregation, particularly in what concerns the calculated X-ray spectra.

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Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena

Cited by 21 publications

References 201 publications

Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

A review on mechanical and material characterisation through molecular dynamics using large-scale atomic/molecular massively parallel simulator (LAMMPS)

Concentration Fluctuation/Microheterogeneity Duality Illustrated with Aqueous 1,4-Dioxane Mixtures

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