FoXS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FoXS
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Tool usage distribution map

This map represents all the scientific publications referring to FoXS per scientific context
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Associated diseases

This word cloud represents FoXS usage per disease context
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Protocols

FoXS specifications

Information


Unique identifier OMICS_10455
Name FoXS
Alternative name Fast X-Ray Scattering
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Type PDB code of input molecule or upload files in PDB format (zip file with several PDBs can be uploaded).
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Andrej Sali

Information


Unique identifier OMICS_10455
Name FoXS
Alternative name Fast X-Ray Scattering
Interface Web user interface
Restrictions to use None
Input data Type PDB code of input molecule or upload files in PDB format (zip file with several PDBs can be uploaded).
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Andrej Sali

Publications for Fast X-Ray Scattering

FoXS citations

 (72)
call_split

Structures of monomeric and oligomeric forms of the Toxoplasma gondii perforin like protein 1

2018
Sci Adv
PMCID: 5943054
PMID: 29750191
DOI: 10.1126/sciadv.aaq0762
call_split See protocol

[…] xible linker between the MACPF domain and APCβ domain acting as rigid bodies. In total, about 10,000 models were generated (), and the SAXS profile was then calculated for each conformation using the FoXS method (). The multistate models were enumerated in MultiFoXS using the branch-and-bound method. To characterize the range of conformations consistent with the SAXS data, we analyzed distribution […]

call_split

Structure of prothrombin in the closed form reveals new details on the mechanism of activation

2018
Sci Rep
PMCID: 5811608
PMID: 29440720
DOI: 10.1038/s41598-018-21304-1
call_split See protocol

[…] ation and then aligned and averaged using DAMAVER. Computing of the theoretical scattering profile of proTCC and proTΔ154-167 and fitting of the experimental profile was performed using the webserver FoXS. […]

call_split

Pro metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+ binding

2018
Nat Commun
PMCID: 5802723
PMID: 29410444
DOI: 10.1038/s41467-018-02859-z
call_split See protocol

[…] eling by Gasbor and Dammif, followed by averaging ten models by DAMAVER. For L230, the missing loop and N-terminal His-tag were modeled using MODELLER implemented in chimera. The best model fitted in FoXS with better χ2 score was used to fit in ab initio SAXS envelope. Results are from triplicate biological samples in a single experiment. Analysis was performed once. The SAXS parameters and result […]

library_books

RNA force field with accuracy comparable to state of the art protein force fields

2018
Proc Natl Acad Sci U S A
PMCID: 5816156
PMID: 29378935
DOI: 10.1073/pnas.1713027115

[…] Two hundred frames were randomly picked from each of the Mg–C, K–C, and K–E ensembles and converted to individual PDB files. The FoXS program () was used to calculate the SAXS profiles of these three model ensembles. The resulting theoretical scattering curves were then fitted to the experimental scattering curves of the Mg(+) […]

call_split

The C terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility

2018
Nucleic Acids Res
PMCID: 5829636
PMID: 29385534
DOI: 10.1093/nar/gky031
call_split See protocol

[…] atomic distances. The χ2 values, Rg values and Dmax values obtained from the three replicates for each simulation were nearly identical.Minimal ensemble searches were carried out five times using the FoXS (Fast X-ray Scattering) server with 100 randomly chosen structures from the LD simulations in order to select the combination of one, two, three, four and five structures that best fit the experi […]

library_books

Structure and mechanism of a bacterial t6A biosynthesis system

2018
Nucleic Acids Res
PMCID: 5814804
PMID: 29309633
DOI: 10.1093/nar/gkx1300

[…] P(r) functions were calculated using the program GNOM (). Theoretical scattering curves were computed from different structural models and compared to experimental scattering curves using the program FoXS (). The relative Porod volume was determined from the SAXS data using DATPOROD, and the molecular mass was determined using DATMOW () and SAXS-MoW (HTTP://www.if.sc.usp.br/∼saxs/). Normal mode an […]


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FoXS institution(s)
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, CA, USA

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