FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

Dina Schneidman-Duhovny; Michal Hammel; John A Tainer; Andrej Sali

doi:10.1093/nar/gkw389

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

Nucleic Acids Res. 2016 Jul 8;44(W1):W424-9. doi: 10.1093/nar/gkw389. Epub 2016 May 5.

Authors

Dina Schneidman-Duhovny¹, Michal Hammel², John A Tainer³, Andrej Sali⁴

Affiliations

¹ Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, CA 94143, USA dina.schneidman@mail.huji.ac.il.
² Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
³ Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
⁴ Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, CA 94143, USA sali@salilab.org.

Abstract

Small Angle X-ray Scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. Here, we describe three web servers for modeling atomic structures based on SAXS profiles. FoXS (Fast X-Ray Scattering) rapidly computes a SAXS profile of a given atomistic model and fits it to an experimental profile. FoXSDock docks two rigid protein structures based on a SAXS profile of their complex. MultiFoXS computes a population-weighted ensemble starting from a single input structure by fitting to a SAXS profile of the protein in solution. We describe the interfaces and capabilities of the servers (salilab.org/foxs), followed by demonstrating their application on Interleukin-33 (IL-33) and its primary receptor ST2.

MeSH terms

Interleukin-1 Receptor-Like 1 Protein / chemistry
Interleukin-33 / chemistry
Internet
Models, Molecular*
Multiprotein Complexes / chemistry*
Proteins / chemistry*
Scattering, Small Angle*
Software*
X-Ray Diffraction*

Substances

Interleukin-1 Receptor-Like 1 Protein
Interleukin-33
Multiprotein Complexes
Proteins

Abstract

MeSH terms

Substances

Grants and funding