Computational protocol: Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis

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Protocol publication

[…] Australian Synchrotron beam specific software SCATTERBRAIN was utilized for SAXS data reduction (including radial integration of the SAXS images and conversion to 1-d dat files). The scattering data from samples were background-subtracted (DATOP) using scattering data taken after the flow through had cleared the column. Due to the presence of overlapping peaks in some of the SEC profiles, the recently developed software US-SOMO (Ultrascan Solution Modeler) HPLC SAS module was employed (,). In summary, the SAXS data were converted to the time domain, Gaussian fitting and deconvolution applied, and scattering data then back generated and used for further analyses. ATSAS programs () were used for further analyses which included calculation of pairwise distribution functions [P(r)], ab initio structure calculation using DAMMIF and DAMAVER (,) and multiphase modeling using MONSA (). Normalized Kratky plots were calculated using the DATGNOM fitted scattering curves with a script written by MCJW. For analyses of the complexes of FL-RIG-I with 10 bp and 8 bp, the ensemble optimization method (EOM) () was used. […]

Pipeline specifications

Software tools ATSAS, DAMMIF, MONSA, EOM
Application Small-angle scattering
Organisms Dipturus trachyderma
Chemicals Adenosine Diphosphate, Adenosine Triphosphate, Tretinoin