Pepsi-SAXS : an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

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Grudinin , Sergei ; Garkavenko , Maria ; Kazennov , Andrei (2017)
  • Publisher: International Union of Crystallography
  • Related identifiers: doi: 10.1107/S2059798317005745
  • Subject: [ SDV.BBM.BP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics | [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation | multipole expansion | Pepsi-SAXS | small-angle scattering | [ MATH.MATH-MP ] Mathematics [math]/Mathematical Physics [math-ph] | [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM]

International audience; 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 χ2 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.
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