RBDmap specifications

Information


Unique identifier OMICS_24190
Name RBDmap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.0.17
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Matthias Hentze <>
  • person_outline Alfredo Castello <>

Publications for RBDmap

RBDmap in publications

 (4)
PMCID: 5827114
PMID: 29483512
DOI: 10.1038/s41467-018-03182-3

[…] binds to a broad range of mrna targets by recognition of a diverse set of sequences,,,,. as a first step to identifying the domains of syncrip engaged in rna binding in living cells, we used the rbdmap data set. these data report on rna-binding protein segments making contact with poly-adenylated rnas within native protein–rna complexes. they are obtained by applying ultraviolet […]

PMCID: 5947564
PMID: 29341429
DOI: 10.1002/wrna.1465

[…] bind to rna. two recent studies have mapped rna binding sites to intrinsically disordered globular regions within rbps, termed noncanonical rbds, using alternative techniques based on rbp‐capture (rbdmap; castello et al., ); and photoactivatable nucleoside analogue incorporation (rbr‐id; he et al., ). although the nature of rbdmap may induce bias towards polyadenlyated rna and rbr‐id may […]

PMCID: 5570134
PMID: 28575444
DOI: 10.1093/nar/gkx460

[…] results provide new details regarding degenerate rna-binding that contrasts from or compares favorably to conclusions drawn by recent comprehensive studies. a proteome-wide map of rna-binding sites, rbdmap, recovered several novel examples of rgg/rg peptides bound to cellular rnas and rgg3 of fus was chosen for validation as representative of these disordered rbds (). published iclip […]

PMCID: 4674897
PMID: 26656258
DOI: 10.1038/srep18054

[…] in the future it may be possible to extend this analysis by corroborating x-ray crystal structure data with data from mrna interactome capture methods and even more refined techniques such as rbdmap (matthias hentze, personal communication)., this work follows on from and expands upon results and methodologies of previous studies examining how structurally derived nucleobase-amino acid […]


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RBDmap institution(s)
European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Department of Biochemistry, University of Oxford, Oxford, UK; CECAD Research Center, University of Cologne, Cologne, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
RBDmap funding source(s)
Supported by MRC Career Development Award no. MR/L019434/1, a ERC Advanced Grant ERC-2011-ADG_20110310, the Virtual Liver Network of the German Ministry for Science and Education and by an EMBO postdoctoral fellowship (LTF1006-2013).

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