Brookes Emre, Rocco Mattia
Department of Biochemistry, University of Texas at San Antonio Health Center, San Antonio, TX, USA.
Biopolimeri e Proteomica, Ospedale Policlinico San Martino, Largo R. Benzi 10, Genova, 16132, Italy.
Eur Biophys J. 2018 Oct;47(7):855-864. doi: 10.1007/s00249-018-1296-0. Epub 2018 Mar 28.
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.
UltraScan解决方案建模器（US-SOMO）是一套全面的、公共领域的、开源的计算机程序套件，主要围绕流体动力学建模以及小角散射（SAS）数据分析与模拟。在此，我们描述自其上次正式发布（#3087，2017年）以来所实现的进展，这些进展可从版本#3141获取，适用于Windows、Linux和Mac操作系统。一项主要工作是从传统的Qt3跨平台软件开发和用户界面库过渡到现代的Qt5版本。除了改进的图形支持外，这还使得能够在所有操作系统上直接实现最新的、速度快了近两个数量级的ZENO流体动力学计算算法。结合SoMo生成的具有重叠的珠子模型，ZENO可从可用的原子级结构提供最精确的平移摩擦计算（Rocco和Byron，《欧洲生物物理杂志》44:417 - 431，2015a），计算时间与其他方法相当或更快。此外，它还使我们能够将结构中的每个原子直接表示为一个（水合）珠子，开启了有趣的新建模可能性。在该套件的小角散射（SAS）部分，已实现一种间接傅里叶变换贝叶斯算法，用于从SAS数据计算成对距离分布函数。最后，最近升级的SAS HPLC模块具有改进的基线校正和对未基线分辨峰的高斯分解以及先进的统计评估工具（Brookes等人，《应用晶体学杂志》49:1827 - 1841，2016），现在允许自动选择顶部峰帧并进行平均。
