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Protocols

CORAL specifications

Information


Unique identifier OMICS_29091
Name CORAL
Alternative name COmplexes with RAndom Loops
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Registration required Yes
Maintained Yes

Maintainers


  • person_outline Dmitri I. Svergun
  • person_outline Daniel Franke

Information


Unique identifier OMICS_29091
Name CORAL
Alternative name COmplexes with RAndom Loops
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
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

Publications for COmplexes with RAndom Loops

CORAL citations

 (5)
library_books

Combined roles of ATP and small hairpin RNA in the activation of RIG I revealed by solution based analysis

2018
Nucleic Acids Res
PMCID: 5887321
PMID: 29346611
DOI: 10.1093/nar/gkx1307

[…] >√3 sRg and approaching zero at higher sRg. This reflects an ordered and compact conformation of DC-RIG-I after binding with 10 bp.To obtain structural models of DC-RIG-I/10 bp ±ATP analogues, CORAL (COmplexes with RAndom Loops) was used, which is based on rigid body modeling of complexes with flexible created missing loops against the SAXS data and allows for the inclusion of coordinates for RNA. […]

call_split

Evidence That the C Terminal Domain of a Type B PutA Protein Contributes to Aldehyde Dehydrogenase Activity and Substrate Channeling

2014
Biochemistry
PMCID: 4159212
PMID: 25137435
DOI: 10.1021/bi500693a
call_split See protocol

[…] CORAL (COmplexes with RAndom Loops) of the ATSAS package was used to determine the structural relationship between the catalytic core and the CTDUF of RcPutA. The default settings of CORAL were used for all […]

library_books

The PHD and Chromo Domains Regulate the ATPase Activity of the Human Chromatin Remodeler CHD4

2012
J Mol Biol
PMCID: 3437443
PMID: 22575888
DOI: 10.1016/j.jmb.2012.04.031

[…] ase domain itself, and using the available high-resolution structures of these individual domains, we performed rigid-body modeling using the SAXS data of the PP-CC construct using the program CORAL (COmplexes with RAndom Loops) (). The model generated fits the data (χ = 1.1) and overlays well with the zigzag ab initio shape envelope generated independently (). In this model, the tandem PHD and ch […]

call_split

Structural Analysis of the C Terminal Region (Modules 18–20) of Complement Regulator Factor H (FH)

2012
PLoS One
PMCID: 3289644
PMID: 22389686
DOI: 10.1371/journal.pone.0032187
call_split See protocol

[…] perposition of available bead models on three-dimensional structures of FH18–20 or FH19–20, as appropriate, were carried out using the program SUPCOMB13 . Rigid body modeling using the program CORAL (Complexes with Random Loops) was also conducted using the FH18–20 crystal structure, constraining either FH modules 18 and 19, or 19 and 20 as fixed, and refining the relative position and orientation […]

library_books

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

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

[…] mizing steric clashes and discontinuities in the chains. BUNCH is particularly well adapted to multidomain proteins with disordered regions between the globular domains. An extension of BUNCH, CORAL (COmplexes with RAndom Loops), is now available, which performs the same modeling but for complexes composed of several partners. If known, distance restraints between residues, such as the interacting […]

Citations

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CORAL 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
CORAL 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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