ArticleEuropean biophysics journal : EBJ2010
The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule.
Article in European biophysics journal : EBJ, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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59 citing papers in PubMed.
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- Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.Biophysical journal · 2024Article
- Strong non-ideality effects at low protein concentrations: considerations for elongated proteins.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
- Modelling the structure of Short Gastrulation and generation of a toolkit for studying its function in Drosophila.Biology open · 2022Article
- A database of calculated solution parameters for the AlphaFold predicted protein structures.Scientific reports · 2022Article
- Early midcell localization of Escherichia coli PBP4 supports the function of peptidoglycan amidases.PLoS genetics · 2022Article
- Probing the oligomeric re-assembling of bacterial fimbriae in vitro: a small-angle X-ray scattering and analytical ultracentrifugation study.European biophysics journal : EBJ · 2021Article
- Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways.eLife · 2021Article
- The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+ machine that can switch between oligomeric states.Nucleic acids research · 2020Article
- Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES.Nucleic acids research · 2020Article
- Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli.The EMBO journal · 2020Article
- Internal cleavage and synergy with twisted gastrulation enhance BMP inhibition by BMPER.Matrix biology : journal of the International Society for Matrix Biology · 2019Article
- Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations.International journal of molecular sciences · 2019Article
- Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite.European biophysics journal : EBJ · 2018Article
- GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.Biophysical journal · 2018Article
- Modeling the Early Stages of Phase Separation in Disordered Elastin-like Proteins.Biophysical journal · 2018Article
- Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.Nucleic acids research · 2018Article
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Abstract
The interpretation of solution hydrodynamic data in terms of macromolecular structural parameters is not a straightforward task. Over the years, several approaches have been developed to cope with this problem, the most widely used being bead modeling in various flavors. We report here the implementation of the SOMO (SOlution MOdeller; Rai et al. in Structure 13:723-734, 2005) bead modeling suite within one of the most widely used analytical ultracentrifugation data analysis software packages, UltraScan (Demeler in Modern analytical ultracentrifugation: techniques and methods, Royal Society of Chemistry, UK, 2005). The US-SOMO version is now under complete graphical interface control, and has been freed from several constraints present in the original implementation. In the direct beads-per-atoms method, virtually any kind of residue as defined in the Protein Data Bank (e.g., proteins, nucleic acids, carbohydrates, prosthetic groups, detergents, etc.) can be now represented with beads whose number, size and position are all defined in user-editable tables. For large structures, a cubic grid method based on the original AtoB program (Byron in Biophys J 72:408-415, 1997) can be applied either directly on the atomic structure, or on a previously generated bead model. The hydrodynamic parameters are then computed in the rigid-body approximation. An extensive set of tests was conducted to further validate the method, and the results are presented here. Owing to its accuracy, speed, and versatility, US-SOMO should allow to fully take advantage of the potential of solution hydrodynamics as a complement to higher resolution techniques in biomacromolecular modeling.
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