RPF

RPF evaluates the agreement between protein 3D structures and experimental NOESY peak lists and resonance assignment data to provide quantitative assessments of NMR structure quality.

Key Features:

• RECALL, PRECISION, F‑MEASURE: Uses RECALL, PRECISION, and F‑MEASURE to compute global NMR structure quality scores that quantify goodness-of-fit to experimental NOESY and assignment data.
• Discrimination Power (DP) score: Computes a DP score that estimates accuracy by quantifying how significantly a query structure differs from random coil models when fitted to NMR chemical shifts and unassigned NOESY data.
• NOESY and resonance assignment comparison: Assesses alignment of query 3D structures with experimental NOESY peak lists and resonance assignment data.
• Local quality mapping: Maps local structure quality measures onto 3D protein coordinates and corresponding NMR spectra to localize discrepancies between model and data.
• Support for unassigned NOESY and chemical shift data: Incorporates unassigned NOESY peak lists and NMR chemical shift information into scoring and comparison procedures.

Scientific Applications:

• NMR structure validation: Provides quantitative validation of protein NMR structures by measuring agreement with NOESY peak lists and resonance assignments.
• Structure and peak-list refinement: Guides refinement of protein models and NOESY peak lists by identifying local mismatches between structure and experimental spectra.
• Accuracy prediction: Predicts relative structure accuracy versus random coil conformations using the DP score.
• Spectrum-based diagnostics: Enables localization of spectral assignment or modeling errors by mapping quality metrics onto NMR spectra and 3D coordinates.

Methodology:

Computes RECALL, PRECISION, and F‑MEASURE to generate global quality scores; computes a Discrimination Power (DP) score by comparing fitted structures to random coil models using NMR chemical shifts and unassigned NOESY data; maps local quality measures onto 3D coordinates and corresponding NMR spectra.