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SCT: a suite of programs for comparing atomistic models with small-angle scattering data

Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged...

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Detalles Bibliográficos
Autores principales: Wright, David W., Perkins, Stephen J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4453981/
https://www.ncbi.nlm.nih.gov/pubmed/26089768
http://dx.doi.org/10.1107/S1600576715007062
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author Wright, David W.
Perkins, Stephen J.
author_facet Wright, David W.
Perkins, Stephen J.
author_sort Wright, David W.
collection PubMed
description Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.
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spelling pubmed-44539812015-06-18 SCT: a suite of programs for comparing atomistic models with small-angle scattering data Wright, David W. Perkins, Stephen J. J Appl Crystallogr Computer Programs Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct. International Union of Crystallography 2015-05-09 /pmc/articles/PMC4453981/ /pubmed/26089768 http://dx.doi.org/10.1107/S1600576715007062 Text en © Wright and Perkins 2015 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Computer Programs
Wright, David W.
Perkins, Stephen J.
SCT: a suite of programs for comparing atomistic models with small-angle scattering data
title SCT: a suite of programs for comparing atomistic models with small-angle scattering data
title_full SCT: a suite of programs for comparing atomistic models with small-angle scattering data
title_fullStr SCT: a suite of programs for comparing atomistic models with small-angle scattering data
title_full_unstemmed SCT: a suite of programs for comparing atomistic models with small-angle scattering data
title_short SCT: a suite of programs for comparing atomistic models with small-angle scattering data
title_sort sct: a suite of programs for comparing atomistic models with small-angle scattering data
topic Computer Programs
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4453981/
https://www.ncbi.nlm.nih.gov/pubmed/26089768
http://dx.doi.org/10.1107/S1600576715007062
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