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RCI specifications

Information


Unique identifier OMICS_17109
Name RCI
Alternative name Random Coil Index
Interface Web user interface
Restrictions to use None
Input format BMRB NMR-STAR or NEF or SHIFTY
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline David Wishart <>

Information


Unique identifier OMICS_17109
Name RCI
Alternative name Random Coil Index
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline David Wishart <>

Publication for Random Coil Index

RCI in pipelines

 (2)
2014
PMCID: 4184797
PMID: 25279835
DOI: 10.1371/journal.pone.0108415

[…] and side chain analysis. in addition comparative analysis of the mup family employed promals3d , for secondary structure driven sequence alignment and multiprot for homologous structure alignment. random coil index (rci) analysis was through the rci webserver . the castp programme was used to measure cavity size and the programmes pic , pdbepisa and ligplot measured intramolecular […]

2012
PMCID: 3441751
PMID: 23028322
DOI: 10.1371/journal.ppat.1002923

[…] domain fold was carried out using scop ; alignment of the cs-domain family employed promals3d for secondary structure-driven sequence alignment and multiprot for homologous structure alignment. random coil index (rci) analysis was carried out using the rci webserver ., the structure of the n1 domain (n1pilq419–514) could not be determined using conventional methods due to the low number […]


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RCI in publications

 (23)
PMCID: 5792643
PMID: 29386631
DOI: 10.1038/s41598-018-20290-8

[…] calculated disordered content with increasing temperature, a behaviour that directly contrasts with that seen for most fully folded (not idp) proteins., neighbour corrected random coil indexing (rci), which uses chemical shift information to predict flexibility within a protein, suggests a region of increased order between residues 746–759 in tarp726–825, which corresponds to a deviation […]

PMCID: 5814841
PMID: 29294091
DOI: 10.1093/nar/gkx1275

[…] and backbone dihedral angles. a set of 199 dihedral angles (table ) for the residues located in the well-ordered regions of the protein core, as defined by nmr relaxation experiments and the rci (random coil index) approach (), were obtained from the analysis of the 1hn, 1hα, 15n, 13cα, 13cβ and 13c’ chemical shifts using the talos+ software (). 1577 noes, used as distance restraints […]

PMCID: 5925765
PMID: 29281006
DOI: 10.1093/bioinformatics/btx785

[…] for spin system assignments (); (iv) visualize chemical shift referencing analysis by the lacs algorithm ();(v) visualize hydrophobic core residues predicted from pacsy database (; ); (vi) visualize rci s2 (random coil index order parameter; ); and/or (vii) generate pine probabilistic labels and accept the most probable ones with p > 0.5 (). then the completeness counter (two-letter-code cm) […]

PMCID: 5717278
PMID: 29208936
DOI: 10.1038/s41598-017-17259-4

[…] reference chemical shift values for the same residues in the oxidized state were obtained from bmrb 11019 (table ). protein flexibility and secondary structure was predicted by comparing the random coil index values from the backbone chemical shifts (hn, n, cα and cβ) (fig. ). based on the analyzed residues it can be deduced that reduction of hcox17 results in the loss […]

PMCID: 5718880
PMID: 29174494
DOI: 10.1016/j.str.2017.10.009

[…] “aliasing,” and these need to be corrected to achieve valid data deposition. finally, for entries containing polypeptides, the amino acid sequence and chemical shift information is used by the rci software () to calculate a random coil index (rci) for each residue, which estimates how likely the residue is to be disordered. in a bar-graph representation of rci for each polypeptide chain, […]


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RCI institution(s)
Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
RCI funding source(s)
Supported by the Natural Sciences and Engineering Research Council (NSERC) and by the Protein Engineering Network of Centres of Excellence (PENCE).

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