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Protocols

Fast-SAXS specifications

Information


Unique identifier OMICS_10456
Name Fast-SAXS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline ANMPathway

Publication for Fast-SAXS

Fast-SAXS citations

 (6)
library_books

Metal cofactor modulated folding and target recognition of HIV 1 NCp7

2018
PLoS One
PMCID: 5929515
PMID: 29715277
DOI: 10.1371/journal.pone.0196662

[…] demonstrated by , in which we showed the SAXS profiles calculated based on the sampled snapshots with (B) and without (C) the inter-domain contacting interactions at saturated zinc concentration. The Fast-SAXS-pro method was used to compute the SAXS profiles of NCp7 from the sampled coarse-grained conformations []. The SAXS profiles calculated based on the structure ensemble by solution NMR (PDB c […]

library_books

Specialized interfaces of Smc5/6 control hinge stability and DNA association

2017
Nat Commun
PMCID: 5290277
PMID: 28134253
DOI: 10.1038/ncomms14011

[…] running the program in ‘slow' mode. Subsequently, DAMCLUST was used to cluster the models into groups, and then to identify individual models that best represented each grouping. Analysis with FoXS (Fast SAXS Profile Computation with Debye Formula) indicated that a single representative dummy atom model, from the largest cluster of 27 related models (deviation 0.61), provided the best overall fit […]

call_split

Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics Monte Carlo Simulations

2016
PLoS One
PMCID: 4881967
PMID: 27227775
DOI: 10.1371/journal.pone.0156043
call_split See protocol

[…] y 4 ps in the MD simulation trajectory, and the decoys are saved after each MC judgment for results analysis. To make a MC judgment, the SAXS intensity profile for a given structure is computed using Fast-SAXS-pro[]. The acceptance probability in the MC judgment is given by the Metropolis criterion[], i.e., min{exp[-(En-En-1]/kBT), 1}. Here, T is the simulation temperature, kB is the Boltzmann con […]

library_books

Modeling the Structure of RNA Molecules with Small Angle X Ray Scattering Data

2013
PLoS One
PMCID: 3817170
PMID: 24223750
DOI: 10.1371/journal.pone.0078007

[…] ucture landscape .Existing approaches can be supplemented by experimental information from SAXS by adding a final step of filtering generated models to those best fitting the experimental data, as in FAST-SAXS RNA , .Attempts have been made to produce an approximate model of flexible RNA molecules using residual dipolar coupling (RDC) data acquired from nuclear magnetic resonance (NMR) experiments […]

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

[…] the same profile using χ, but cannot compare the fit of one model against two different experimental profiles.To assess the performance of different profile calculation programs (Zernike polynomials, Fast-SAXS, AquaSAXS, CRYSOL and FoXS), we compute the theoretical scattering for a model protein glucose isomerase [PDB:2G4J] (Figure ) and fit it to the experimental profile. A high accuracy SAXS pro […]

library_books

How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective

2012
PMCID: 3394175
PMID: 22044150
DOI: 10.2174/138920312799277901

[…] f the hydration water []. Other methods cleverly use a coarse-grain approach, taking advantage of the low-resolution of SAXS and significantly decreasing the computation time. Among them, the program Fast-SAXS (available at: http://thallium.bsd.uchicago.edu/ RouxLab/saxs.html) [,] proposes a more realistic description of the water shell based entirely on the atomistic description of water using mo […]

Citations

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Fast-SAXS institution(s)
Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA
Fast-SAXS funding source(s)
This work was supported by the National Institute of Health through grant No. CA-093577 and by a joint grant from the University of Chicago Cancer Center and Argonne National Laboratory (grant No. UCCC/ANL).

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