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

Research output: Contribution in Book/Catalog/Report/Conference proceedingChapter

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.
Original languageEnglish
Title of host publicationInnovations in Computational Chemistry
Subtitle of host publicationTheoretical and Quantum Chemistry at the Dawn of the 21st Century
EditorsRamon Carbó-Dorca, Tanmoy Chakraborty
Pages197-248
Number of pages51
Publication statusPublished - 2018

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

Keywords

  • Smoothing
  • Discretization
  • Denoising
  • Coarse Graining
  • Spline
  • Gaussian Convolution
  • Wavelets
  • Multiresolution Analysis
  • Vector Quantization
  • Electron Density
  • Charge Density
  • Molecular Similarity
  • Molecular Dynamics
  • Point Charge
  • Protein
  • Ubiquitin

Cite this

Leherte, L. (2018). Applications of Leveling Methods to Properties of Small Molecules and Protein Systems. In R. Carbó-Dorca, & T. Chakraborty (Eds.), Innovations in Computational Chemistry: Theoretical and Quantum Chemistry at the Dawn of the 21st Century (pp. 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. editor / Ramon Carbó-Dorca ; Tanmoy Chakraborty. 2018. pp. 197-248
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Leherte, L 2018, Applications of Leveling Methods to Properties of Small Molecules and Protein Systems. in R Carbó-Dorca & T Chakraborty (eds), Innovations in Computational Chemistry: Theoretical and Quantum Chemistry at the Dawn of the 21st Century. pp. 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.

Research output: Contribution in Book/Catalog/Report/Conference proceedingChapter

TY - CHAP

T1 - Applications of Leveling Methods to Properties of Small Molecules and Protein Systems

AU - Leherte, Laurence

PY - 2018

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AB - 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.

KW - Smoothing

KW - Discretization

KW - Denoising

KW - Coarse Graining

KW - Spline

KW - Gaussian Convolution

KW - Wavelets

KW - Multiresolution Analysis

KW - Vector Quantization

KW - Electron Density

KW - Charge Density

KW - Molecular Similarity

KW - Molecular Dynamics

KW - Point Charge

KW - Protein

KW - Ubiquitin

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M3 - Chapter

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BT - Innovations in Computational Chemistry

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