FoXS: a web server for rapid computation and fitting of SAXS profiles

By Dina Schneidman-Duhovny, M. Hammel, Andrej Sali. 2010

523 citations recorded by the source corpus.

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).

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective (2012, methodology): “html) uses the Debye formula to calculate intensities from atomic factors to which it adds a term that represents the displaced solvent and another term proportional to the solvent accessible surface to generate the contribution of the hydration water [92].”
Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, methodology): “16,17 20 CASP12 included both CLMS and SAXS data.”
Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade (2022, unknown): “, 2021) and AllosModFoXS (Schneidman-Duhovny et al., 2010; Weinkam et al., 2012) following previously established protocols (Ando et al.”
UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “Thus, a good use of an experimental SAXS proﬁle is to compare it to a proﬁle computed from a 3D structural model that was derived from other data (Pons et al., 2010; Schneidman-Duhovny et al., 2010; Svergun et al., 1995).”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “FoXS (http://salilab.org/foxs/; Schneidman-Duhovny et al., 2010) calculates a Small Angle X-ray Scattering (SAXS) profile for an uploaded protein structure and compares it with an experimental profile.”
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles (2016, background): “FoXS is a webserver that performs this task (13,23).”
Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies (2012, background): “, and FoXS for computing a SAXS profile of a given structure”
Integrative structure modeling with the Integrative Modeling Platform (2017, methodology): “…of their assembly, 31 scoring protein-ligand interactions, 49 combining multiple SAXS profiles, 50 comparing a structure with the corresponding SAXS profile, 51–53 or enriching pairwise docking using SAXS data, 52 and can be used through web interfaces, from Chimera, 54 or from the command line.”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “FoXS ( http://salilab.org/foxs/ ; Schneidman-Duhovny et al., 2010) calculates a Small Angle X-ray Scattering (SAXS) proﬁle for an uploaded protein structure and compares it with an experimental proﬁle.”
Computational design of trimeric influenza neutralizing proteins targeting the hemagglutinin receptor binding site (2017, methodology): “Consistency of the models with the experimental SAXS data was analyzed with the FoXS webserver 50, 51 .”