Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite

• Published in: European biophysics journal 2018-10, Vol.47 (7), p.855-864
• Main Authors: Brookes, Emre, Rocco, Mattia
• Format: Article
• Language: English
• Subjects: Algorithms; Atomic structure; Bayesian analysis; Biochemistry; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Cell Biology; Computation; Computer applications; Computer programs; Computer simulation; Data analysis; Data processing; Distribution functions; Fourier transforms; High-performance liquid chromatography; Life Sciences; Liquid chromatography; Mathematical models; Membrane Biology; Nanotechnology; Neurobiology; Operating systems; Original Article; Public domain; Scattering; Simulation; Software; Source code
• ISSN: 0175-7571; 1432-1017
• DOI: 10.1007/s00249-018-1296-0

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.