Applications of Leveling Methods to Properties of Small Molecules and Protein Systems

Résultats de recherche: Contribution dans un livre/un catalogue/un rapport/dans les actes d'une conférenceChapitre

Résumé

Despite the advent of high performance computing resources, calculations applied to large systems may remain intractable. Methods to reduce the level of details are therefore essential to allow fast calculations, but also to provide new insights into the systems under study. In this paper, various techniques and application domains related to the leveling of molecular properties through low-resolution, smoothing, denoising, or coarse-graining approaches, are presented. A focus is done on Gaussian smoothing, wavelet multi-resolution analysis, crystallography-based methods, as well as discretization methods. An emphasis is given on the use of smoothed charge density distribution functions and their extrema to generate reduced point charge models (RPCM) of proteins. Molecular dynamics simulations based on RPCMs are reported for three Ubiquitin complexes. Results are discussed based on the ability of such models to generate stable protein-ligand conformations.
langue originaleAnglais
titreInnovations in Computational Chemistry
Sous-titreTheoretical and Quantum Chemistry at the Dawn of the 21st Century
rédacteurs en chefRamon Carbó-Dorca, Tanmoy Chakraborty
Pages197-248
Nombre de pages51
étatPublié - 2018

Empreinte digitale

Multiresolution analysis
Molecules
Crystallography
Ubiquitin
Charge density
Probability density function
Distribution functions
Conformations
Molecular dynamics
Proteins
Ligands
Computer simulation

mots-clés

    Citer ceci

    Leherte, L. (2018). Applications of Leveling Methods to Properties of Small Molecules and Protein Systems. Dans R. Carbó-Dorca, & T. Chakraborty (eds.), Innovations in Computational Chemistry: Theoretical and Quantum Chemistry at the Dawn of the 21st Century (p. 197-248)
    Leherte, Laurence. / Applications of Leveling Methods to Properties of Small Molecules and Protein Systems. Innovations in Computational Chemistry: Theoretical and Quantum Chemistry at the Dawn of the 21st Century. Editeur / Ramon Carbó-Dorca ; Tanmoy Chakraborty. 2018. p. 197-248
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    abstract = "Despite the advent of high performance computing resources, calculations applied to large systems may remain intractable. Methods to reduce the level of details are therefore essential to allow fast calculations, but also to provide new insights into the systems under study. In this paper, various techniques and application domains related to the leveling of molecular properties through low-resolution, smoothing, denoising, or coarse-graining approaches, are presented. A focus is done on Gaussian smoothing, wavelet multi-resolution analysis, crystallography-based methods, as well as discretization methods. An emphasis is given on the use of smoothed charge density distribution functions and their extrema to generate reduced point charge models (RPCM) of proteins. Molecular dynamics simulations based on RPCMs are reported for three Ubiquitin complexes. Results are discussed based on the ability of such models to generate stable protein-ligand conformations.",
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    Leherte, L 2018, Applications of Leveling Methods to Properties of Small Molecules and Protein Systems. Dans R Carbó-Dorca & T Chakraborty (eds), Innovations in Computational Chemistry: Theoretical and Quantum Chemistry at the Dawn of the 21st Century. p. 197-248.

    Applications of Leveling Methods to Properties of Small Molecules and Protein Systems. / Leherte, Laurence.

    Innovations in Computational Chemistry: Theoretical and Quantum Chemistry at the Dawn of the 21st Century. Ed. / Ramon Carbó-Dorca; Tanmoy Chakraborty. 2018. p. 197-248.

    Résultats de recherche: Contribution dans un livre/un catalogue/un rapport/dans les actes d'une conférenceChapitre

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    Leherte L. Applications of Leveling Methods to Properties of Small Molecules and Protein Systems. Dans Carbó-Dorca R, Chakraborty T, rédacteurs en chef, Innovations in Computational Chemistry: Theoretical and Quantum Chemistry at the Dawn of the 21st Century. 2018. p. 197-248