ArticleEuropean biophysics journal : EBJ2018
Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite.
Article in European biophysics journal : EBJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain.Protein science : a publication of the Protein Society · 2025Article
- Structural Insights into Plant Viruses Revealed by Small-Angle X-ray Scattering and Atomic Force Microscopy.Viruses · 2024Review
- AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank.Journal of applied crystallography · 2023Article
- SDS-induced hexameric oligomerization of myotoxin-II from Bothrops asper assessed by sedimentation velocity and nuclear magnetic resonance.European biophysics journal : EBJ · 2023Article
- Investigation of dynamic solution interactions between NET-1 and UNC-5B by multi-wavelength analytical ultracentrifugation.European biophysics journal : EBJ · 2023Article
- Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures.European biophysics journal : EBJ · 2023Article
- 2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data.Acta crystallographica. Section D, Structural biology · 2023Article
- Molecular Determinants of Fibrillation in a Viral Amyloidogenic Domain from Combined Biochemical and Biophysical Studies.International journal of molecular sciences · 2022Article
- Non-canonical Staphylococcus aureus pathogenicity island repression.Nucleic acids research · 2022Article
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- Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium.BMC biology · 2022Article
- Modelling the structure of Short Gastrulation and generation of a toolkit for studying its function in Drosophila.Biology open · 2022Article
- Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase.Biophysical journal · 2022Article
- A database of calculated solution parameters for the AlphaFold predicted protein structures.Scientific reports · 2022Article
- Experimental Evidence of Intrinsic Disorder and Amyloid Formation by theInternational journal of molecular sciences · 2022Article
- Identification of a Region in the Common Amino-terminal Domain of Hendra Virus P, V, and W Proteins Responsible for Phase Transition and Amyloid Formation.Biomolecules · 2021Article
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Abstract
The UltraScan SOlution MOdeller (US-SOMO) is a comprehensive, public domain, open-source suite of computer programs centred on hydrodynamic modelling and small-angle scattering (SAS) data analysis and simulation. We describe here the advances that have been implemented since its last official release (#3087, 2017), which are available from release #3141 for Windows, Linux and Mac operating systems. A major effort has been the transition from the legacy Qt3 cross platform software development and user interface library to the modern Qt5 release. Apart from improved graphical support, this has allowed the direct implementation of the newest, almost two-orders of magnitude faster version of the ZENO hydrodynamic computation algorithm for all operating systems. Coupled with the SoMo-generated bead models with overlaps, ZENO provides the most accurate translational friction computations from atomic-level structures available (Rocco and Byron Eur Biophys J 44:417-431, 2015a), with computational times comparable with or faster than those of other methods. In addition, it has allowed us to introduce the direct representation of each atom in a structure as a (hydrated) bead, opening interesting new modelling possibilities. In the small-angle scattering (SAS) part of the suite, an indirect Fourier transform Bayesian algorithm has been implemented for the computation of the pairwise distance distribution function from SAS data. Finally, the SAS HPLC module, recently upgraded with improved baseline correction and Gaussian decomposition of not baseline-resolved peaks and with advanced statistical evaluation tools (Brookes et al. J Appl Cryst 49:1827-1841, 2016), now allows automatic top-peak frame selection and averaging.
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