Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles
Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles
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DOI：
10.1107/s2059798317005745
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发表时间：
2017-05-01
影响因子：
2.2
通讯作者：
Kazennov, Andrei
中科院分区：
文献类型：
--
作者：
Grudinin, Sergei;Garkavenko, Maria;Kazennov, Andrei
提出了一种称为 Pepsi-SAXS 的新方法，可根据原子模型计算小角度 X 射线散射剖面。该方法基于多极展开方案，与其他测试方法相比速度明显更快。特别是，使用 Nyquist-Shannon-Kotelnikov 采样定理，多极展开阶数适应模型的大小和实验数据的分辨率。有人认为，通过使用自适应展开阶数，该方法对模型中原子数量具有与基于德拜的方法相同的二次依赖性，但计算复杂度方面的前置因子要小得多。该方法已在从 BioIsis 和 SASBDB 数据库收集的 50 多个模型中得到系统验证。使用笔记本电脑证明，在对 BioIsis 数据库的数据进行测试时，与 CRYSOL、FoXS 和 SAStbx 中的三维 Zernike 方法相比，Pepsi-SAXS 的速度分别快约 7、29 和 36 倍；在对来自 SASBDB 的数据进行测试时，与 CRYSOL、FoXS 和 SAStbx 相比，分别快约 5、21 和 25 倍。平均而言，在 BioIsis 和 SASBDB 配置文件上进行测试时，Pepsi-SAXS 在 chi(2) 方面表现出与 CRYSOL 和 FoXS 相当的准确性。加上可调参数允许的小变化，这证明了该方法的有效性。 Pepsi-SAXS 可在 http://team.inria.fr/nano-d/software/pepsi-saxs 上购买。
A new method called Pepsi-SAXS is presented that calculates small-angle X-ray scattering profiles from atomistic models. The method is based on the multipole expansion scheme and is significantly faster compared with other tested methods. In particular, using the Nyquist-Shannon-Kotelnikov sampling theorem, the multipole expansion order is adapted to the size of the model and the resolution of the experimental data. It is argued that by using the adaptive expansion order, this method has the same quadratic dependence on the number of atoms in the model as the Debye-based approach, but with a much smaller prefactor in the computational complexity. The method has been systematically validated on a large set of over 50 models collected from the BioIsis and SASBDB databases. Using a laptop, it was demonstrated that Pepsi-SAXS is about seven, 29 and 36 times faster compared with CRYSOL, FoXS and the three-dimensional Zernike method in SAStbx, respectively, when tested on data from the BioIsis database, and is about five, 21 and 25 times faster compared with CRYSOL, FoXS and SAStbx, respectively, when tested on data from SASBDB. On average, Pepsi-SAXS demonstrates comparable accuracy in terms of chi(2) to CRYSOL and FoXS when tested on BioIsis and SASBDB profiles. Together with a small allowed variation of adjustable parameters, this demonstrates the effectiveness of the method. Pepsi-SAXS is available at http://team.inria.fr/nano-d/software/pepsi-saxs.