Monte Carlo-based rigid body modelling of large protein complexes against small angle scattering data

2010 ◽  
Vol 34 (3) ◽  
pp. 158-164 ◽  
Author(s):  
Christian Meesters ◽  
Bruno Pairet ◽  
Anja Rabenhorst ◽  
Heinz Decker ◽  
Elmar Jaenicke
Keyword(s):  
Monte Carlo ◽  
Rigid Body ◽  
Small Angle ◽  
Protein Complexes ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Large Protein ◽  
Angle Scattering

scholarly journals Improvements and considerations for size distribution retrieval from small-angle scattering data by Monte Carlo methods

2013 ◽  
Vol 46 (2) ◽  
pp. 365-371 ◽  
Author(s):  
Brian R. Pauw ◽  
Jan Skov Pedersen ◽  
Samuel Tardif ◽  
Masaki Takata ◽  
Bo B. Iversen
Keyword(s):  
Monte Carlo ◽  
Small Angle ◽  
Free Particle ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Convergence Criterion ◽  
Size Distributions ◽  
Trial And Error ◽  
Angle Scattering ◽  
Scattering Measurement

Monte Carlo (MC) methods, based on random updates and the trial-and-error principle, are well suited to retrieve form-free particle size distributions from small-angle scattering patterns of non-interacting low-concentration scatterers such as particles in solution or precipitates in metals. Improvements are presented to existing MC methods, such as a non-ambiguous convergence criterion, nonlinear scaling of contributions to match their observability in a scattering measurement, and a method for estimating the minimum visibility threshold and uncertainties on the resulting size distributions.

ORNL_SAS: software for calculation of small-angle scattering intensities of proteins and protein complexes

2007 ◽  
Vol 40 (4) ◽  
pp. 782-785 ◽  
Author(s):  
Elina Tjioe ◽  
William T. Heller
Keyword(s):  
Small Angle ◽  
Model Building ◽  
Protein Complexes ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Contrast Variation ◽  
X Ray ◽  
Angle Scattering ◽  
Intensity Calculation

The programORNL_SAScalculates solution small-angle X-ray and neutron scattering intensity profiles from a wide variety of structures, including atomic-resolution models of proteins and protein complexes, low-resolution models defined in any manner, or combinations of both.ORNL_SASis capable of simultaneously generating multiple intensity profiles, such as a contrast-variation series, and evaluating the quality of the fit of the model profiles to experimental data in a single run of the program. The capabilities of the widely applicable approach make it possible to useORNL_SASas the intensity calculation engine of model-building applications for small-angle scattering data.

scholarly journals Ligand-Induced Conformational Changes in Tissue Transglutaminase: Monte Carlo Analysis of Small-Angle Scattering Data

2000 ◽  
Vol 78 (6) ◽  
pp. 3240-3251 ◽  
Author(s):  
Paolo Mariani ◽  
Flavio Carsughi ◽  
Francesco Spinozzi ◽  
Sandro Romanzetti ◽  
Gerd Meier ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Conformational Changes ◽  
Small Angle ◽  
Tissue Transglutaminase ◽  
Monte Carlo Analysis ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Angle Scattering

Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data

2010 ◽  
Vol 403 (2) ◽  
pp. 217-230 ◽  
Author(s):  
Carles Pons ◽  
Marco D’Abramo ◽  
Dmitri I. Svergun ◽  
Modesto Orozco ◽  
Pau Bernadó ◽  
...  
Keyword(s):  
Structural Characterization ◽  
Small Angle ◽  
Protein Complexes ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Computational Docking ◽  
Angle Scattering

scholarly journals 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

2017 ◽  
Vol 73 (9) ◽  
pp. 710-728 ◽  
Author(s):  
Jill Trewhella ◽  
Anthony P. Duff ◽  
Dominique Durand ◽  
Frank Gabel ◽  
J. Mitchell Guss ◽  
...  
Keyword(s):  
Small Angle ◽  
Task Force ◽  
Data Bank ◽  
Small Angle Scattering ◽  
Scattering Data ◽  
Quality Data ◽  
Angle Scattering ◽  
Publication Guidelines ◽  
Guidelines And Recommendations

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

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