Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jul;38(Web Server issue):W540-4.
doi: 10.1093/nar/gkq461. Epub 2010 May 27.

FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles

Affiliations
Free PMC article

FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles

Dina Schneidman-Duhovny et al. Nucleic Acids Res. .
Free PMC article

Abstract

Small angle X-ray scattering (SAXS) is an increasingly common technique for low-resolution structural characterization of molecules in solution. SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can contribute to many applications, such as comparing a conformation in solution with the corresponding X-ray structure, modeling a flexible or multi-modular protein, and assembling a macromolecular complex from its subunits. These applications require rapid computation of a SAXS profile from a molecular structure. FoXS (Fast X-Ray Scattering) is a rapid method for computing a SAXS profile of a given structure and for matching of the computed and experimental profiles. Here, we describe the interface and capabilities of the FoXS web server (http://salilab.org/foxs).

Figures

Figure 1.
Figure 1.
Snapshot of a FoXS output page. Computed profiles of two PDB files are compared to the experimental SAXS profile of malic enzyme (data from http://bioisis.net/, PF1026). The first structure (pdb_model) includes a model of the unfolded His tag region (35 residues), while the second structure (2dvm) does not. The server was run with the default parameters and the hydration layer modeling was disabled. Plots on the left display the theoretical profiles and plots on the right display their fit to the experimental profile. The top two plots are for the structure with the modeled unfolded region (pdb_model), the middle two plots are for the original PDB file (2dvm), the bottom left plot overlay the profiles for the two input structures, and the bottom right plot shows their fit to the experimental profile. The structure with the modeled unfolded region shows a better fit to the experimental profile with the value of χ = 2.88, compared to χ = 6.33 for the original crystallographic structure. The user can follow the links to download the computed profiles and their fittings.

Similar articles

See all similar articles

Cited by 225 articles

See all "Cited by" articles

References

    1. Koch MH, Vachette P, Svergun DI. Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q. Rev. Biophys. 2003;36:147–227. - PubMed
    1. Petoukhov MV, Svergun DI. Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr. Opin. Struct. Biol. 2007;17:562–571. - PubMed
    1. Putnam CD, Hammel M, Hura GL, Tainer JA. X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys. 2007;40:191–285. - PubMed
    1. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL, 2nd, Tsutakawa SE, Jenney FE, Jr, Classen S, Frankel KA, Hopkins RC, et al. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) Nat. Methods. 2009;6:606–612. - PMC - PubMed
    1. Tiede DM, Mardis KL, Zuo X. X-ray scattering combined with coordinate-based analyses for applications in natural and artificial photosynthesis. Photosynth. Res. 2009;102:267–279. - PMC - PubMed

Publication types

Feedback