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Citations per year

Number of citations per year for the bioinformatics software tool FoXSDock
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FoXSDock specifications

Information


Unique identifier OMICS_10451
Name FoXSDock
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input is two proteins and a SAXS profile of their complex.
Output data The output is a list of potential complexes sorted by a score that combines interface energy and the fit to SAXS profile.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Dina Schneidman-Duhovny

Information


Unique identifier OMICS_10451
Name FoXSDock
Interface Web user interface
Restrictions to use None
Input data The input is two proteins and a SAXS profile of their complex.
Output data The output is a list of potential complexes sorted by a score that combines interface energy and the fit to SAXS profile.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Dina Schneidman-Duhovny

Publication for FoXSDock

FoXSDock citations

 (4)
library_books

Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components

2018
Nat Commun
PMCID: 5758563
PMID: 29311576
DOI: 10.1038/s41467-017-02570-5

[…] unction and may be important for other roles of Suv3.Fig. 3We next used the SAXS data for the fl-Cg-Dss-Suv3183–699 complex to independently verify the arrangement of the complex subunits. We applied FoxsDock to dock Cg-Suv3183–699 to fl-Cg-Dss1 and obtained multiple models with various placements of Cg-Dss1 and Cg-Suv3. The model that corresponded to the orientation of both components that was ob […]

library_books

Combining NMR and small angle X ray scattering for the study of biomolecular structure and dynamics

2017
PMCID: 5553349
PMID: 28501583
DOI: 10.1016/j.abb.2017.05.005

[…] related with a closed Gα conformation induced by GTP .The combination of SAXS and NMR has also been successfully applied in the field of molecular docking. The programs HADDOCK , , pyDockSAXS , , and FoXSDock have been developed for robust screening of ligand binding and complex formation and include scoring functions for SAXS data. It has been shown that the incorporation of SAXS data yields sig […]

library_books

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

2016
Nucleic Acids Res
PMCID: 4987932
PMID: 27151198
DOI: 10.1093/nar/gkw389

[…] requently suffer from large errors, due to protein flexibility and inaccurate scoring functions. SAXS profile of the complex can significantly improve the success rate of protein–protein docking (,). FoXSDock is a web server for protein–protein docking restrained by a SAXS profile of the complex; the input to FoXSDock is the structures of the docked proteins in the PDB format and a SAXS profile of […]

library_books

Integrative structural modeling with small angle X ray scattering profiles

2012
BMC Struct Biol
PMCID: 3427135
PMID: 22800408
DOI: 10.1186/1472-6807-12-17

[…] h docking programs, energy based scoring functions, and a SAXS fit score. pyDockSAXS uses FTDock [] for sampling complex orientations, pyDock [] for energy-based scoring, and CRYSOL for SAXS scoring. FoXSDock uses PatchDock [] for orientation sampling, FireDock [] for refinement and energy-based scoring, and FoXS for SAXS scoring. Both methods nearly double the success rate relative to docking alo […]


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FoXSDock 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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