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Protocols

GASBOR specifications

Information


Unique identifier OMICS_29290
Name GASBOR
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.3
Stability Stable
Requirements
ATSAS
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Daniel Franke

Additional information


https://www.embl-hamburg.de/biosaxs/manuals/gasbor.html

Publications for GASBOR

GASBOR citations

 (157)
library_books

Structural basis for the recognition of complex type N glycans by Endoglycosidase S

2018
Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] ) were computed using GNOM. The molecular mass was determined using ScÅter,. The low-resolution structures of EndoSD233A/E235L in presence and absence of G2 product were calculated ab initio by using GASBOR. The results and statistics are summarized in Supplementary Table . […]

library_books

C1q and Mannose Binding Lectin Interact with CR1 in the Same Region on CCP24 25 Modules

2018
Front Immunol
PMCID: 5845983
PMID: 29563915
DOI: 10.3389/fimmu.2018.00453

[…] lexibility that could be mainly attributed to the presence of the glycans, but also to the C-terminal histidine tag and to the semi-flexible linker. The overall ab initio envelopes, calculated by the GASBOR software, show two elongated blobs with a global boomerang shape (Figures D–E). Temptatively, one could attribute the larger blob to the CCP24 which is slightly bigger in size and also bears tw […]

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

[…] re previously collected at the beamline 12-ID-B of the Advanced Photon Source at Argonne National Laboratory (Argonne, IL) on protWT (0.5–5 mg/ml). The low-resolution envelope was produced using both GASBOR (q up to 0.8 Å−1) and DAMMIN (q up to 0.3 Å−1) by directly fitting the reciprocal space scattering profile. Twenty models were generated for every calculation and then aligned and averaged usin […]

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

[…] and Porod volume and exponent. The pair distribution plot P(r) was converted using Gnom program to estimate Dmax (maximum dimension), and the output Gnom file was used for ab initio shape modeling 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 […]

library_books

Biophysical insights from a single chain camelid antibody directed against the Disrupted in Schizophrenia 1 protein

2018
PLoS One
PMCID: 5764400
PMID: 29324815
DOI: 10.1371/journal.pone.0191162

[…] l values from atomic coordinates. The distance distribution function p(r) was determined using the program DATGNOM []. For each dataset, 20 ab initio reconstructions were generated using DAMMIF [] or GASBOR [], followed by averaging and filtering in DAMAVER []. The resulting consensus models were used in further analyses. For the purposes of fitting and visualization, they were converted into volu […]

call_split

Signaling ammonium across membranes through an ammonium sensor histidine kinase

2018
Nat Commun
PMCID: 5764959
PMID: 29323112
DOI: 10.1038/s41467-017-02637-3
call_split See protocol

[…] extraction was performed using PRIMUS. Evaluation of the real-space distance distribution function, p(r), was performed using GNOM. Subsequent ab initio model building was carried out using DAMMIN or GASBOR. Analyses of potential conformational transitions in the HK domain were conducted using an elastic network procedure implemented in the program SREFLEX and homology models for the HK transducin […]

Citations

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GASBOR institution(s)
European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany; Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Moscow, Russia; N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Moscow, Russia; N.N. Semenov Institute of Chemical Physics of Russian Academy of Sciences, Moscow, Russia; National Research Centre ‘Kurchatov Institute’, Moscow, Russia; Department of Chemical Engineering, Stanford University, Stanford, CA, USA
GASBOR funding source(s)
Supported by FP7 Research Infrastructures (award Nos. Biostruct-X [283570], IDPbyNMR [264257], iNEXT [653706]); BMBF (award Nos. BIOSCAT [05K12YE1], TT-SAS [05K16YEA]); HFSP (award No. RGP0017/2012); DFG/GACR (award No. 9/5-1).

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