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PREDITOR specifications

Information


Unique identifier OMICS_10808
Name PREDITOR
Interface Web user interface
Restrictions to use None
Input data PREDITOR accepts three kinds of input files: (i) chemical shift assignments in BMRB NMR-STAR format, (ii) chemical shift assignments in SHIFTY format and (iii) raw protein sequence in FASTA format.
Input format BMRB NMR-STAR, SHIFTY, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline David Wishart <>

Publication for PREDITOR

PREDITOR in publications

 (8)
PMCID: 5667893
PMID: 29040325
DOI: 10.1371/journal.ppat.1006686

[…] [, ]. spectra were recorded on a varian inova 600 mhz spectrometer, processed with nmrpipe [], and analyzed using the tools in sparky []. chemical shift indices were calculated using the program preditor []. normalized chemical shift changes were calculated as described []., the trim5α coiled-coil/l2/spry model was built as described in the main text, using pymol software (schrödinger […]

PMCID: 5292684
PMID: 28165000
DOI: 10.1038/srep41662

[…] be assigned for 74 and 96 residues in the ntd and ctd, respectively., in-house inca program was used for noe assignment and structure calculation. phi/psi angles were predicted using talos+ and preditor softwares. backbone hydrogen bonds constraints were identified by recording a 2d 15n-1h hsqc experiment 1 h after solubilisation in d2o of the lyophilized 15n-labelled protein. the 20 lowest […]

PMCID: 3973705
PMID: 24695525
DOI: 10.1371/journal.pone.0093228

[…] peaks were classified into strong (1.8–2.7 å), medium (1.8–3.3 å), weak (2.3–4.5 å), and very weak (2.8–5.5 å) . backbone dihedral restraints were obtained from the chemical shift data using the preditor protocol . the hydrogen-bond (h-bond) restraints of 1.5–2.5 å for rhn-o and 2.3–3.2 å for rn-o were applied in the final stages of the refinement. simulated annealing (sa) calculations […]

PMCID: 3919607
PMID: 24234454
DOI: 10.1093/nar/gkt1091

[…] were deposited in the biological magnetic resonance data bank under the reference 18959., for peptide structure calculation, torsion angle restraints for the ψ, ϕ and χ1 angles were derived from preditor analysis () and distance restraints were derived from noesy spectra using the automated procedure of cyana 2.1 (). then, distance and angle restraints were used for water-refinement of 200 […]

PMCID: 3728621
PMID: 23908768
DOI: 10.7554/eLife.00813.032

[…] change upon binding to a calcium ion.10.7554/elife.00813.026table 4.*sidechains coordinating the ca2+ ion in ef hands 1 and 2 were implemented as distance restraints.†χ1 angles were obtained from preditor (), and ϕ and ψ angles were calculated using talos+ ().‡the r.m.s differences (hz) between the experimental rdc data and back-calculated rdcs from the 10 lowest energy structures […]


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PREDITOR institution(s)
Department of Computing Science, University of Alberta Edmonton, AB, Canada; Department of Biological Sciences, University of Alberta Edmonton, AB, Canada; NRC National Institute for Nanotechnology (NINT), Edmonton AB, Canada
PREDITOR funding source(s)
Funding for this project was provided by the Protein Engineering Network of Centres of Excellence (PENCE), the Natural Sciences and Engineering Research Council (NSERC), the National Research Council (NINT) and Genome Alberta (a division of Genome Canada).

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