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Protocols

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 citations

 (12)
library_books

TRIM5α SPRY/coiled coil interactions optimize avid retroviral capsid recognition

2017
PLoS Pathog
PMCID: 5667893
PMID: 29040325
DOI: 10.1371/journal.ppat.1006686

[…] HSQC [, ]. 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 []. […]

library_books

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid state Nuclear Magnetic Resonance Spectroscopy

2017
PMCID: 5752270
PMID: 28994783
DOI: 10.3791/55779

[…] d proline residues might show unusual chemical shift values, as they often act as "secondary structure breakers". Predict the protein dihedral angles from the assigned chemical shifts using TALOS+ or PREDITOR. The predicted Phi/Psi dihedral angles reflect the secondary structure of the protein subunit and are used as structural restraints throughout the modeling process. Use 13Cα, 13Cβ chemical sh […]

library_books

High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid

2017
Sci Rep
PMCID: 5292684
PMID: 28165000
DOI: 10.1038/srep41662

[…] 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 […]

library_books

Cullin3 BTB Interface: A Novel Target for Stapled Peptides

2015
PLoS One
PMCID: 4388676
PMID: 25848797
DOI: 10.1371/journal.pone.0121149

[…] ded in the cyana library. The structures were analyzed and visualized by using the program MOLMOL [] and PROCHECK [].The dihedral angles were estimated using HN and Hα chemical shifts by the software PREDITOR[]. The secondary structure propensity has been evaluated based on the HN and Hα chemical shifts using the software Secondary Structure Propensity (SSP)[]. […]

library_books

Homodimerization of RBPMS2 through a new RRM interaction motif is necessary to control smooth muscle plasticity

2014
Nucleic Acids Res
PMCID: 4150794
PMID: 25064856
DOI: 10.1093/nar/gku692

[…] ydrogen bond was enforced using two distance restraints: d(NH,O) = 1.8–2.3 Å and d(N,O) = 2.7–3.3 Å. The backbone dihedral angle restraints Φ and Ψ were derived from chemical shift analysis using the PREDITOR program (). Side chain dihedral angle restraints (χ1, χ2) were derived from detailed analysis of the proton NOE network and inspection of COSY/TOCSY peak intensities between Hα/Hβ protons, ta […]

call_split

Solution Structure of CXCL5 — A Novel Chemokine and Adipokine Implicated in Inflammation and Obesity

2014
PLoS One
PMCID: 3973705
PMID: 24695525
DOI: 10.1371/journal.pone.0093228
call_split See protocol

[…] ross 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 with e […]


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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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