Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform

A novel computational method based on atomic form factors and the fast Fourier transform (FFT) is developed to compute small- and near-wide-angle X-ray scattering profiles of biomacromolecules from explicit solvent modeling. The method is validated by comparing the results with those from non-FFT ap...

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Main Authors: Tong, Dudu, Yang, Jianbin, Lu, Lanyuan
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2015
Subjects:
Online Access:https://hdl.handle.net/10356/81221
http://hdl.handle.net/10220/39189
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-812212023-02-28T16:58:06Z Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform Tong, Dudu Yang, Jianbin Lu, Lanyuan School of Biological Sciences X-ray solution scattering Small-angle X-ray scattering (SAXS) Wide-angle X-ray scattering (WAXS) Proteins Structural dynamics A novel computational method based on atomic form factors and the fast Fourier transform (FFT) is developed to compute small- and near-wide-angle X-ray scattering profiles of biomacromolecules from explicit solvent modeling. The method is validated by comparing the results with those from non-FFT approaches and experiments, and good agreement with experimental data is observed for both small and near-wide angles. In terms of computational efficiency, the FFT-based method is advantageous for protein solution systems of more than 3000 atoms. Furthermore, the computational cost remains nearly constant for a wide range of system sizes. The FFT-based approach can potentially handle much larger molecular systems compared with popular existing methods. MOE (Min. of Education, S’pore) Published version 2015-12-21T06:46:08Z 2019-12-06T14:25:52Z 2015-12-21T06:46:08Z 2019-12-06T14:25:52Z 2015 Journal Article Tong, D., Yang, J., & Lu, L. (2015). Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform. Journal of Applied Crystallography, 48, 1834-1842. 1600-5767 https://hdl.handle.net/10356/81221 http://hdl.handle.net/10220/39189 10.1107/S1600576715018816 en Journal of Applied Crystallography © 2015 International Union of Crystallography. This paper was published in Journal of Applied Crystallography and is made available as an electronic reprint (preprint) with permission of International Union of Crystallography. The published version is available at: [http://dx.doi.org/10.1107/S1600576715018816]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. 9 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic X-ray solution scattering
Small-angle X-ray scattering (SAXS)
Wide-angle X-ray scattering (WAXS)
Proteins
Structural dynamics
spellingShingle X-ray solution scattering
Small-angle X-ray scattering (SAXS)
Wide-angle X-ray scattering (WAXS)
Proteins
Structural dynamics
Tong, Dudu
Yang, Jianbin
Lu, Lanyuan
Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform
description A novel computational method based on atomic form factors and the fast Fourier transform (FFT) is developed to compute small- and near-wide-angle X-ray scattering profiles of biomacromolecules from explicit solvent modeling. The method is validated by comparing the results with those from non-FFT approaches and experiments, and good agreement with experimental data is observed for both small and near-wide angles. In terms of computational efficiency, the FFT-based method is advantageous for protein solution systems of more than 3000 atoms. Furthermore, the computational cost remains nearly constant for a wide range of system sizes. The FFT-based approach can potentially handle much larger molecular systems compared with popular existing methods.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Tong, Dudu
Yang, Jianbin
Lu, Lanyuan
format Article
author Tong, Dudu
Yang, Jianbin
Lu, Lanyuan
author_sort Tong, Dudu
title Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform
title_short Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform
title_full Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform
title_fullStr Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform
title_full_unstemmed Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform
title_sort modeling solution x-ray scattering of biomacromolecules using an explicit solvent model and the fast fourier transform
publishDate 2015
url https://hdl.handle.net/10356/81221
http://hdl.handle.net/10220/39189
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