Ultrathin tunable conducting oxide films for near-IR applications: an introduction to spectroscopy shape theory

Villarreal–Rios, A L; Bedoya-Calle, Álvaro; Caro-Lopera, Francisco J.; Ortiz-Méndez, Ubaldo; García-Méndez, Manuel; Pérez-Ramírez, F. O.

doi:10.1007/s42452-019-1569-y

Cited by 5 publications

(15 citation statements)

References 28 publications

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“…and the remaining n − 2 atoms are rigidly translated to the addressed coordinates p j (3) , j = 1, ..., n; j ≠ w,t from (1). Part (3): For a more meaningful docking along the segment of atoms p w (3) and p t (3) , ( 3) is restricted such that…”

Section: Methods and Algorithmsmentioning

confidence: 99%

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Shape Theory Applied to Molecular Docking and Automatic Localization of Ligand Binding Pockets in Large Proteins

et al. 2022

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Automatic search of cavities and binding mode analysis between a ligand and a 3D protein receptor are challenging problems in drug design or repositioning. We propose a solution based on a shape theory theorem for an invariant coupled system of ligand−protein. The theorem provides a matrix representation with the exact formulas to be implemented in an algorithm. The method involves the following results: (1) exact formulae for the shape coordinates of a located-rotated invariant coupled system; (2) a parameterized search based on a suitable domain of van der Waals radii; (3) a scoring function for the discrimination of sites by measuring the distance between two invariant coupled systems including the atomic mass; (4) a matrix representation of the Lennard-Jones potential type 6−12 and 6−10 as the punctuation function of the algorithm for a molecular docking; and (5) the optimal molecular docking as a solution of an optimization problem based on the exploration of an exhaustive set of rotations. We apply the method in the xanthine oxidase protein with the following ligands: hypoxanthine, febuxostat, and chlorogenic acid. The results show automatic cavity detection and molecular docking not assisted by experts with meaningful amino acid interactions. The method finds better affinities than the expert software for known published cavities.

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Section: Methods and Algorithmsmentioning

confidence: 99%

“…with b > 0 (eq 2). r > 0 is a real parameter in a certain appropriate interval, (g,h), varying in a suitable domain of the van der Waals radius, according to the atoms located at l u (3) ,l v (3) ,p w (3) ,p t (3) . The q possible ligand−protein invariant…”

Section: Methods and Algorithmsmentioning

confidence: 99%

Shape Theory Applied to Molecular Docking and Automatic Localization of Ligand Binding Pockets in Large Proteins

et al. 2022

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“…[36]. Recently, Riemannian distance has been used in experimental physics and chemistry studies in order to discriminate populations on plasma physics evolution [57], determination of equilibrium structures in nanoclusters [58], and spectroscopy shape analysis [59], showing the applicability to scientific studies.…”

Section: Riemannian Full and Partial Procrustes Distances: Definitions And Comparisonmentioning

confidence: 99%

About Validation-Comparison of Burned Area Products

et al. 2020

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This paper proposes a validation-comparison method for burned area (BA) products. The technique considers: (1) bootstrapping of scenes for validation-comparison and (2) permutation tests for validation. The research focuses on the tropical regions of Northern Hemisphere South America and Northern Hemisphere Africa and studies the accuracy of the BA products: MCD45, MCD64C5.1, MCD64C6, Fire CCI C4.1, and Fire CCI C5.0. The first and second parts consider methods based on random matrix theory for zone differentiation and multiple ancillary variables such as BA, the number of burned fragments, ecosystem type, land cover, and burned biomass. The first method studies the zone effect using bootstrapping of Riemannian, full Procrustes, and partial Procrustes distances. The second method explores the validation by using distance permutation tests under uncertainty. The results refer to Fire CCI 5.0 with the best BA description, followed by MCD64C6, MCD64C5.1, MCD45, and Fire CCI 4.1. It was also found that biomass, total BA, and the number of fragments affect the BA product accuracy.

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“…The Gaussian statistics was used extensively [ 17 , 18 ]; now, robust models for shape theory are available for several transformations (affine, polar, SVD, QR) and for real normalized division algebras (real, complex, quaternion, and octonion) [ 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. A crucial concept for our purposes, includes the Riemannian distance (RD) and was applied recently in the following fields: spectroscopic analysis [ 26 ] and rocking curves [ 27 ]; stochastic search of molecules [ 28 ]; and remote sensing of burning satellite products [ 29 ].…”

Section: Introductionmentioning

confidence: 99%

“…IR spectra are a way to assess compounds’ chemical stability and physical capacity [ 30 ], with rapid quantification allowing the collection of specific molecular fingerprints from samples [ 31 ]. These capabilities and the shape theory allow a complete characterization of the compounds [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Mechanism of Antioxidant Activity of Betanin, Betanidin and Respective C15-Epimers via Shape Theory, Molecular Dynamics, Density Functional Theory and Infrared Spectroscopy

et al. 2022

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Betanin and betanidin are compounds with extensive interest; they are effectively free radical scavengers. The present work aims to elucidate the differences between the mechanism of the antioxidant activity of betanin, betanidin, and their respective C15-epimers. Shape Theory establishes comparisons between the molecules’ geometries and determines parallelisms with the descriptors BDE, PA, ETE IP, PDE, and infrared spectra (IR) obtained from the molecule simulations. Furthermore, the molecules were optimized using the B3LYP/6-31+G(d,p) protocol. Finally, the molecular docking technique analyzes the antioxidant activity of the compounds in the complex with the therapeutic target xanthine oxidase (XO), based on a new proposal for the geometrical arrangement of the ligand atoms in the framework of Shape Theory. The results obtained indicate that the SPLET mechanism is the most favorable in all the molecules studied and that the first group that loses the hydrogen atom in the four molecules is the C17COOH, presenting less PA the isobetanidin. Furthermore, regarding the molecular docking, the interactions of these compounds with the target were favorable, standing out to a greater extent the interactions of isobetanidin with XO, which were analyzed after applying molecular dynamics.

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Ultrathin tunable conducting oxide films for near-IR applications: an introduction to spectroscopy shape theory

Cited by 5 publications

References 28 publications

Shape Theory Applied to Molecular Docking and Automatic Localization of Ligand Binding Pockets in Large Proteins

Shape Theory Applied to Molecular Docking and Automatic Localization of Ligand Binding Pockets in Large Proteins

About Validation-Comparison of Burned Area Products

Mechanism of Antioxidant Activity of Betanin, Betanidin and Respective C15-Epimers via Shape Theory, Molecular Dynamics, Density Functional Theory and Infrared Spectroscopy

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