Please cite the following if you use this work in your publications:
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Paper on which SAXS-A-FOLD is based:
Brookes, E., Rocco, M., Vachette, P. & Trewhella, J. (2023). AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank. J. Appl. Crystallogr. 56, 910-926. DOI: 10.1107/S1600576723005344 -
Paper describing the SAXS-A-FOLD website:
Brookes, E., Curtis, J., Householder, A. & Rocco, M. (2025). SAXS-A-FOLD: a website for fast ensemble modeling optimizing the fit of AlphaFold or user-supplied protein structures with flexible regions to SAXS data. J. Appl. Crystallogr. Submitted. -
MMC paper:
Curtis, J. E., Raghunandan, S., Nanda, H. & Krueger, S. (2012). SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints. Comput. Phys. Commun. 183, 382–389. DOI: 10.1016/j.cpc.2011.09.010 -
WAXSiS paper:
Knight, C. J. & Hub, J. S. (2015). WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics. Nucleic Acids Res. 43, W225–W230. DOI: 10.1093/nar/gkv309
For the Compute I(q)/P(r) phase, please cite the following depending on the method(s) used:
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CRYSOL:
Manalastas-Cantos, K., Konarev, P.V., Hajizadeh, N.R., Kikhney, A.G., Petoukhov, M.V., Molodenskiy, D.S., Panjkovich, A., Mertens, H.D.T., Gruzinov, A., Borges, C., Jeffries, C.M., Svergun, D.I. & Franke, D. (2021). ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J. Appl. Cryst. 50, 1212–1225.
DOI: 10.1107/S1600576720013412 -
PEPSI-SAXS:
Grudinin, S., Garkavenko, M. & Kazennov, A. (2017). Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles. Acta Cryst. D 73, 449–464.
DOI: 10.1107/S2059798317005745