RPF: a quality assessment tool for protein NMR structures

By Yuanpeng Janet Huang, Antonio Rosato, Gautam Singh, Gaetano T. Montelione. 2012

53 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy, Signal Processing

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Citations in the corpus

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “…residue–residue contact areas (Olechnovic et al., 2013), measures using residue contact similarity (Rodrigues et al., 2012) or the recall, precision, F-measure (RPF)/DP score, which was initially developed to evaluate the quality of nuclear magnetic resonance (NMR) structures (Huang et al., 2012).”
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures (2022, methodology): “…as a primary validation tool since its development as a “NMR R factor” in 2005 (Huang et al., 2005; Huang et al., 2006; Raman et al., 2010; Huang et al., 2012; Rosato et al., 2012; Rosato et al., 2013; Rosato et al., 2015; Sala et al., 2019; Huang et al., 2021)…”
Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2 (2021, unknown): “We next assessed how well the NMR and CASP14 structures fit to the experimental NOESY peak list data, using the RPF-DP score.(14,15) For T1029, the plot of DP score versus GDT for all CASP14 predictor groups has a poor correlation (Figure 4D), and DP scores range from – 1.”
Assessment of template based protein structure predictions in CASP10 (2014, methodology): “25–27 The RPF method was adapted here as one of the assessment scores for template-based assessment in CASP10.”
Protein structure determination by combining sparse NMR data with evolutionary couplings (2015, unknown): “RPF-DP scores are correlated with structure accuracy for fully-protonated proteins, with reliable models having DP scores greater than ~ 0.70 – 0.75 18,19 .”