Peakr: simulating solid-state NMR spectra of proteins

Bioinformatics. 2013 May 1;29(9):1134-40. doi: 10.1093/bioinformatics/btt125. Epub 2013 Mar 14.

Abstract

Motivation: When analyzing solid-state nuclear magnetic resonance (NMR) spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, for example, chemical shift predictions and structural models can be of considerable help. Existing solutions are typically limited in the type of experiment they can consider and difficult to adapt to different settings.

Results: Here, we present Peakr, a software to simulate solid-state NMR spectra of proteins. It can generate simulated spectra based on numerous common types of internuclear correlations relevant for assignment and structure elucidation, can compare simulated and experimental spectra and produces lists and visualizations useful for analyzing measured spectra. Compared with other solutions, it is fast, versatile and user friendly.

Availability and implementation: Peakr is maintained under the GPL license and can be accessed at http://www.peakr.org. The source code can be obtained on request from the authors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Conformation
  • Proteins / chemistry*
  • Software*

Substances

  • Proteins