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Related Concept Videos

¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
¹³C NMR: ¹H–¹³C Decoupling01:04

¹³C NMR: ¹H–¹³C Decoupling

The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
NMR Spectrometers: Overview01:20

NMR Spectrometers: Overview

NMR spectrometers consist of a strong magnet, a radiofrequency transmitter, and a detector attached to a computer console for recording spectra of samples containing NMR-active nuclei. In first-generation NMR instruments called continuous-wave spectrometers, the resonance frequencies of the nuclei are determined by frequency-sweep or field-sweep methods. The magnetic field strength is fixed and the rf signal is swept in the former, while the radiofrequency signal is fixed and the magnetic field...
NMR Spectroscopy: Chemical Shift Overview01:15

NMR Spectroscopy: Chemical Shift Overview

The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
For instance, the proton...

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Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins
07:24

Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins

Published on: September 23, 2021

PICKY: a novel SVD-based NMR spectra peak picking method.

Babak Alipanahi1, Xin Gao, Emre Karakoc

  • 1David R.Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, Canada.

Bioinformatics (Oxford, England)
|May 30, 2009
PubMed
Summary

Automated peak picking for Nuclear Magnetic Resonance (NMR) spectra is now possible with PICKY, improving protein structure determination. This method efficiently processes spectra, enabling downstream analysis and high-resolution protein structure calculations.

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Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy (NMR) and Microscale Thermophoresis (MST)
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Published on: November 2, 2018

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Last Updated: Jun 22, 2026

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15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
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Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy (NMR) and Microscale Thermophoresis (MST)
10:28

Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy (NMR) and Microscale Thermophoresis (MST)

Published on: November 2, 2018

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • Automated Nuclear Magnetic Resonance (NMR) peak picking is crucial for protein structure determination but remains a significant challenge.
  • Current manual or semi-automatic methods are laborious, time-consuming, and costly.
  • Accurate peak picking is a prerequisite for resonance assignment, Nuclear Overhauser Effect (NOE) distance restraint assignment, and protein structure calculation.

Purpose of the Study:

  • To develop and systematically evaluate an automated peak picking method for experimental NMR spectra.
  • To address the limitations of manual and semi-automatic peak picking in NMR-based protein structure determination.

Main Methods:

  • Introduced novel techniques including noise-level estimation, component forming and subdivision, and Singular Value Decomposition (SVD)-based peak picking.
  • Developed PICKY, an automated method for peak picking in 2D and 3D NMR spectra.
  • Incorporated peak pruning and refinement steps for enhanced accuracy.

Main Results:

  • PICKY achieved an average recall of 88% and precision of 74% across 32 real spectra from eight proteins.
  • The method demonstrated efficiency, processing an average NMR spectrum in 15.7 seconds.
  • Successfully integrated PICKY-generated peak lists into downstream software (IPASS, SPARTA, FALCON) for automated protein structure calculation, yielding high-resolution structures (e.g., TM1112 at 1.25 Å).

Conclusions:

  • PICKY provides a robust and efficient automated solution for NMR peak picking.
  • The method facilitates the complete automated pipeline for protein structure determination from NMR data.
  • PICKY is available for use and integrates with existing tools like SPARKY for interactive refinement.