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

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

Perkins, SJ; Perkins, SJ; (2015) SCT: a suite of programs for comparing atomistic models to small-angle scattering data. Journal of Applied Crystallography , 48 pp. 953-961. 10.1107/S1600576715007062. Green open access

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Abstract

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.

Type:	Article
Title:	SCT: a suite of programs for comparing atomistic models to small-angle scattering data
Open access status:	An open access version is available from UCL Discovery
DOI:	10.1107/S1600576715007062
Publisher version:	http://dx.doi.org/10.1107/S1600576715007062
Language:	English
Additional information:	This is an open-access article distributed under the terms of the Creative Commons Attribution Licence (http://creativecommons.org/licenses/by/2.0/uk/legalcode), which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Keywords:	analytical ultracentrifugation; constrained modelling; hydration shells; neutron scattering; X-ray scattering
UCL classification:	UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
URI:	https://discovery.ucl.ac.uk/id/eprint/1468272