SREFLEX statistics

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Citations per year

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

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

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Protocols

SREFLEX specifications

Information


Unique identifier OMICS_29097
Name SREFLEX
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Some SAS experimental data files in ascii format containing 3 columns: (1) experimental scattering vector, (2) experimental intensity and (3) experimental errors.
Input format DAT
Computer skills Medium
Stability Stable
Requirements
ATSAS
Registration required Yes
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Dmitri I. Svergun
  • person_outline Daniel Franke

Information


Unique identifier OMICS_29097
Name SREFLEX
Interface Web user interface
Restrictions to use None
Computer skills Basic
Registration required Yes
Maintained Yes

Maintainers


  • person_outline Dmitri I. Svergun
  • person_outline Daniel Franke

Publications for SREFLEX

SREFLEX citations

 (10)
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

[…] solution-scattering profile calculated from the crystal structure (6EN3). Analyses of potential conformational transitions were conducted using an elastic network procedure implemented in the program SREFLEX. The better fit obtained using SREFLEX and the normalized Kratky plot suggest the protein show some flexibility in solution. The maximum dimensions (Dmax), the interatomic distance distributio […]

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

[…] o 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 transducing domain as starting points. Modeling of full-length Ks-Amt5 was done by several approaches. In the first, the program MEMPROT was used to build a coro […]

library_books

Structure and mechanism of a bacterial t6A biosynthesis system

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

[…] ined 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 analysis (NMA) was performed using the program Sreflex () and conformational sampling and multistate modeling were executed in MultiFoXS (). Ab initio envelop reconstruction was performed using the programs DAMMIN () and DAMAVER () in the ATSAS so […]

library_books

Structure of the mouse acidic amino acid decarboxylase GADL1

2018
PMCID: 5947694
PMID: 29372909
DOI: 10.1107/S2053230X17017848

[…] eight was determined by comparison of the forward scattering intensity, I(0), with a fresh monomeric bovine serum albumin standard. Models of MmGADL1 were built with GASBOR (Svergun et al., 2001) and SREFLEX (Panjkovich & Svergun, 2016), using data extrapolated to zero concentration. Theoretical scattering curves from crystal structure coordinates were calculated with CRYSOL (Svergun et al., 1995) […]

library_books

Structural and functional dissection of the DH and PH domains of oncogenic Bcr Abl tyrosine kinase

2017
Nat Commun
PMCID: 5727386
PMID: 29235475
DOI: 10.1038/s41467-017-02313-6

[…] nter concentration effects, such as inter-particle interference using the program PRIMUS from the ATSAS package. GNOM was used to obtain the p(r) and determine the corresponding D max and R g values. SREFLEX was used to generate and refine high-resolution hybrid models using high-resolution structures as the starting point. EOM was used to generate an ensemble of conformations and to assess the in […]

library_books

Structural and molecular comparison of bacterial and eukaryotic trigger factors

2017
Sci Rep
PMCID: 5587573
PMID: 28878399
DOI: 10.1038/s41598-017-10625-2

[…] culated with SUPCOMB or SUPALM . Fits between the SAXS data and the structures were evaluated with CRYSOL and FoXS and superposed with the bead models using SUPALM . The models were improved using SREFLEX in rigid or flexible mode with domain partition. To this end, sequences regions of the domains were determined from the RaptorX model in accordance with the domain annotation of the available […]


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SREFLEX institution(s)
European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany; Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Moscow, Russia; A. 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
SREFLEX 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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