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Citations per year

Number of citations per year for the bioinformatics software tool RCI
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This map represents all the scientific publications referring to RCI per scientific context
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Protocols

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 citations

 (35)
call_split

Causal Inference in the Perception of Verticality

2018
Sci Rep
PMCID: 5882842
PMID: 29615728
DOI: 10.1038/s41598-018-23838-w
call_split See protocol

[…] ltimately be treated as informative of body tilt.24P(xV,xI|C¯)=12πσVσ0∫−∞∞exp(−(xV−Θ)22σV2−Θ22σ02)dΘ×12πσIσ0∫−∞∞exp(−(xI−Θ)22σI2−Θ22σ02)dΘ=12π(σV2+σ02)(σI2+σ02)exp(−12(xV2σV2+σ02+xI2σI2+σ02)).As in,, rCI is a weighted average of the intermediate tilt estimates according to the SS strategy rSS and according to the FF strategy rFF, with weights proportional to the respective probability of the causa […]

library_books

The intrinsically disordered Tarp protein from chlamydia binds actin with a partially preformed helix

2018
Sci Rep
PMCID: 5792643
PMID: 29386631
DOI: 10.1038/s41598-018-20290-8

[…] 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 towa […]

library_books

Structure and function of the N terminal domain of the yeast telomerase reverse transcriptase

2017
Nucleic Acids Res
PMCID: 5814841
PMID: 29294091
DOI: 10.1093/nar/gkx1275

[…] istances 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 in s […]

call_split

PINE SPARKY.2 for automated NMR based protein structure research

2017
Bioinformatics
PMCID: 5925765
PMID: 29281006
DOI: 10.1093/bioinformatics/btx785
call_split See protocol

[…] 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) can […]

library_books

Disulfide driven folding for a conditionally disordered protein

2017
Sci Rep
PMCID: 5717278
PMID: 29208936
DOI: 10.1038/s41598-017-17259-4

[…] chemical shifts were assigned for Ala, Trp and Ser and their neighbouring residues as they have a clear Cβ chemical shifts. Protein flexibility and secondary structure was predicted by comparing the Random Coil index values from the backbone chemical shifts (HN, N, Cα and Cβ).Backbone amide 15N relaxation data (R1, R1ρ and heteronuclear 15N-1H-NOE were measured for hCox17 at 600 MHz by published […]

call_split

Validation of Structures in the Protein Data Bank

2017
PMCID: 5718880
PMID: 29174494
DOI: 10.1016/j.str.2017.10.009
call_split See protocol

[…] ectral “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, ea […]


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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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