RPF: a quality assessment tool for protein NMR structures.

Nucleic Acids Research
Yuanpeng J HuangGaetano T Montelione

Abstract

We describe the RPF web server, a quality assessment tool for protein NMR structures. The RPF server measures the 'goodness-of-fit' of the 3D structure with NMR chemical shift and unassigned NOESY data, and calculates a discrimination power (DP) score, which estimates the differences between the fits of the query structures and random coil structures to these experimental data. The DP-score is an accuracy predictor of the query structure. The RPF server also maps local structure quality measures onto the 3D structure using an online molecular viewer, and onto the NMR spectra, allowing refinement of the structure and/or NOESY peak list data. The RPF server is available at: http://nmr.cabm.rutgers.edu/rpf.

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Citations

Jul 31, 2013·Journal of Biomolecular NMR·Roberto TejeroGaetano T Montelione
Dec 3, 2014·Progress in Nuclear Magnetic Resonance Spectroscopy·Wim F Vranken
Aug 22, 2015·Protein Science : a Publication of the Protein Society·John K EverettGaetano T Montelione
Jan 8, 2014·Journal of the American Chemical Society·Binchen MaoGaetano T Montelione
Dec 11, 2013·Proteins·Yuanpeng J HuangGaetano T Montelione
Jun 18, 2015·Journal of Biomolecular NMR·Yuanpeng Janet HuangGaetano T Montelione
Jun 3, 2015·Journal of Biomolecular NMR·Timothy J RaganGeerten W Vuister
Jun 15, 2015·Journal of Biomolecular NMR·Antonio RosatoGeerten W Vuister
Sep 26, 2013·Current Opinion in Structural Biology·Antonio RosatoGaetano T Montelione
Jun 30, 2015·Nature Methods·Yuefeng TangGaetano T Montelione
Sep 10, 2013·Structure·Gaetano T MontelioneJohn L Markley
Jun 12, 2013·Computational Biology and Chemistry·Anurag BagariaPeter Güntert
Jan 24, 2015·Acta Crystallographica. Section D, Biological Crystallography·Simon P SkinnerGeerten W Vuister
May 9, 2018·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Cailu LinDanielle R Reed
Jul 10, 2018·Bioinformatics·Naohiro KobayashiToshimichi Fujiwara
Sep 1, 2018·Bioinformatics·Kliment OlechnovičČeslovas Venclovas
Jul 28, 2019·Proteins·James C RobertsonAlberto Perez
Oct 12, 2019·Proteins·Davide SalaGaetano T Montelione
Nov 8, 2019·Bioinformatics·Gabriel StuderTorsten Schwede
May 30, 2020·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Melissa RotunnoElizabeth M Gillanders
Dec 20, 2020·Nature Communications·Nicholas J FowlerMike P Williamson
Apr 16, 2020·Biophysical Journal·Davide TavellaFrancesca Massi
Aug 1, 2021·Structure·Nicholas J FowlerMike P Williamson
Jul 14, 2017·Journal of Chemical Information and Modeling·Dániel DudolaZoltán Gáspári

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Methods Mentioned

BETA
Protein NMR
NMR
X-ray

Software Mentioned

Molprobity
Verify3D
PROCHECK
Sparky
Protein Structure Validation Server ( PSVS )
all
Jmol
RPF
Xeasy

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