Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends t...

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Main Authors: Perkins, Stephen J., Wright, David W., Zhang, Hailiang, Brookes, Emre H., Chen, Jianhan, Irving, Thomas C., Krueger, Susan, Barlow, David J., Edler, Karen J., Scott, David J., Terrill, Nicholas J., King, Stephen M., Butler, Paul D., Curtis, Joseph E.
Format: Article
Language:English
Published: International Union of Crystallography 2016
Online Access:http://eprints.nottingham.ac.uk/41955/
http://eprints.nottingham.ac.uk/41955/
http://eprints.nottingham.ac.uk/41955/
http://eprints.nottingham.ac.uk/41955/1/j-49-01861.pdf
id nottingham-41955
recordtype eprints
spelling nottingham-419552017-10-12T22:33:25Z http://eprints.nottingham.ac.uk/41955/ Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS) Perkins, Stephen J. Wright, David W. Zhang, Hailiang Brookes, Emre H. Chen, Jianhan Irving, Thomas C. Krueger, Susan Barlow, David J. Edler, Karen J. Scott, David J. Terrill, Nicholas J. King, Stephen M. Butler, Paul D. Curtis, Joseph E. The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers. International Union of Crystallography 2016-12 Article PeerReviewed application/pdf en cc_by http://eprints.nottingham.ac.uk/41955/1/j-49-01861.pdf Perkins, Stephen J. and Wright, David W. and Zhang, Hailiang and Brookes, Emre H. and Chen, Jianhan and Irving, Thomas C. and Krueger, Susan and Barlow, David J. and Edler, Karen J. and Scott, David J. and Terrill, Nicholas J. and King, Stephen M. and Butler, Paul D. and Curtis, Joseph E. (2016) Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). Journal of Applied Crystallography, 49 (6). pp. 1861-1875. ISSN 1600-5767 http://scripts.iucr.org/cgi-bin/paper?S160057671601517X doi:10.1107/S160057671601517X doi:10.1107/S160057671601517X
repository_type Digital Repository
institution_category Local University
institution University of Nottingham Malaysia Campus
building Nottingham Research Data Repository
collection Online Access
language English
description The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.
format Article
author Perkins, Stephen J.
Wright, David W.
Zhang, Hailiang
Brookes, Emre H.
Chen, Jianhan
Irving, Thomas C.
Krueger, Susan
Barlow, David J.
Edler, Karen J.
Scott, David J.
Terrill, Nicholas J.
King, Stephen M.
Butler, Paul D.
Curtis, Joseph E.
spellingShingle Perkins, Stephen J.
Wright, David W.
Zhang, Hailiang
Brookes, Emre H.
Chen, Jianhan
Irving, Thomas C.
Krueger, Susan
Barlow, David J.
Edler, Karen J.
Scott, David J.
Terrill, Nicholas J.
King, Stephen M.
Butler, Paul D.
Curtis, Joseph E.
Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)
author_facet Perkins, Stephen J.
Wright, David W.
Zhang, Hailiang
Brookes, Emre H.
Chen, Jianhan
Irving, Thomas C.
Krueger, Susan
Barlow, David J.
Edler, Karen J.
Scott, David J.
Terrill, Nicholas J.
King, Stephen M.
Butler, Paul D.
Curtis, Joseph E.
author_sort Perkins, Stephen J.
title Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)
title_short Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)
title_full Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)
title_fullStr Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)
title_full_unstemmed Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)
title_sort atomistic modelling of scattering data in the collaborative computational project for small angle scattering (ccp-sas)
publisher International Union of Crystallography
publishDate 2016
url http://eprints.nottingham.ac.uk/41955/
http://eprints.nottingham.ac.uk/41955/
http://eprints.nottingham.ac.uk/41955/
http://eprints.nottingham.ac.uk/41955/1/j-49-01861.pdf
first_indexed 2018-09-06T13:16:46Z
last_indexed 2018-09-06T13:16:46Z
_version_ 1610864191258755072

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