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: expanded functionality and new tools for small-angle scattering data analysis.

作者信息

Manalastas-Cantos Karen, Konarev Petr V, Hajizadeh Nelly R, Kikhney Alexey G, Petoukhov Maxim V, Molodenskiy Dmitry S, Panjkovich Alejandro, Mertens Haydyn D T, Gruzinov Andrey, Borges Clemente, Jeffries Cy M, Svergun Dmitri I, Franke Daniel

机构信息

European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany.

A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation.

出版信息

J Appl Crystallogr. 2021 Feb 1;54(Pt 1):343-355. doi: 10.1107/S1600576720013412.


DOI:10.1107/S1600576720013412
PMID:33833657
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7941305/
Abstract

The software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the package are described. They include , for simulating isotropic 2D scattering patterns; , to perform operations on 2D images and masks; , a method for variance estimation of structural invariants through parametric resampling; , which computes the pair distance distribution function by a direct Fourier transform of the scattering data; , to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in for Bayesian consensus-based concentration-independent molecular weight estimation; , an shape analysis method that optimizes the search model directly against the scattering data; , an application to set up the initial search volume for multiphase modelling of membrane proteins; , to perform quasi-atomistic modelling of liposomes with elliptical shapes; , which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; , which reconstructs the shape of an unknown intermediate in an evolving system; and and , for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the graphical interface to Qt5, updating - a plugin to run a subset of tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future releases. All these features are implemented in , freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/54254063c60d/j-54-00343-fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/863935d6c2f7/j-54-00343-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/9b474f18d2ac/j-54-00343-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/5930ba0c61a1/j-54-00343-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/c4bd26b32c3d/j-54-00343-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/eac319e65490/j-54-00343-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/b2273eb633f4/j-54-00343-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/2bd977624886/j-54-00343-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/b266af3c08e0/j-54-00343-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/e9abb1dcab1e/j-54-00343-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/54254063c60d/j-54-00343-fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/863935d6c2f7/j-54-00343-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/9b474f18d2ac/j-54-00343-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/5930ba0c61a1/j-54-00343-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/c4bd26b32c3d/j-54-00343-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/eac319e65490/j-54-00343-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/b2273eb633f4/j-54-00343-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/2bd977624886/j-54-00343-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/b266af3c08e0/j-54-00343-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/e9abb1dcab1e/j-54-00343-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aa1c/7941305/54254063c60d/j-54-00343-fig10.jpg

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本文引用的文献

[1]
Restoring structural parameters of lipid mixtures from small-angle X-ray scattering data.

J Appl Crystallogr. 2021-2-1

[2]
Simulation of small-angle X-ray scattering data of biological macromolecules in solution.

J Appl Crystallogr. 2020-2-18

[3]
Structural Kinetics of MsbA Investigated by Stopped-Flow Time-Resolved Small-Angle X-Ray Scattering.

Structure. 2020-3-3

[4]
SASBDB: Towards an automatically curated and validated repository for biological scattering data.

Protein Sci. 2019-10-11

[5]
Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS).

Sci Rep. 2019-8-30

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Curr Opin Struct Biol. 2019-6-13

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Acta Crystallogr D Struct Biol. 2019-4-8

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Acta Crystallogr D Struct Biol. 2018-11-30

[9]
Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.

J Appl Crystallogr. 2018-11-9

[10]
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Protein Sci. 2018-12-13

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