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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

 (45)
library_books

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

2018
PMCID: 5943054
PMID: 29750191
DOI: 10.1126/sciadv.aaq0762

[…] 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 […]

library_books

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

2018
PMCID: 5802723
PMID: 29410444
DOI: 10.1038/s41467-018-02859-z

[…] 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 […]

library_books

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

2018
PMCID: 5829636
PMID: 29385534
DOI: 10.1093/nar/gky031

[…] 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 […]

library_books

Structure and mechanism of a bacterial t6A biosynthesis system

2018
PMCID: 5814804
PMID: 29309633
DOI: 10.1093/nar/gkx1300

[…] 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 […]

library_books

A Consensus Model of Human Apolipoprotein A I in its Monomeric and Lipid free State

2017
PMCID: 5749415
PMID: 29131142
DOI: 10.1038/nsmb.3501

[…] refined iteratively guided by hydrogen-deuterium exchange (h-dx) data published by chetty and colleagues. models were evaluated against experimental data obtained from saxs using the online server foxs,. the final model was subjected to energy minimization using the yasara server and rotamers were manually refined using coot. given the lack of a density map, rotamer position was determined […]

library_books

Three dimensional context rather than NLS amino acid sequence determines importin α subtype specificity for RCC1

2017
PMCID: 5645467
PMID: 29042532
DOI: 10.1038/s41467-017-01057-7

[…] model was then converted to a surface map using the situs program suite. theoretical solution scattering curves of all crystallographic structures determined in this work were calculated using the foxs web server. saxs data collection and analysis statistics are summarized in supplementary table ., analytical sec was carried out on a superpose 12-column equilibrated with gel filtration buffer […]


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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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