title: VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.
abstract: NMR spectroscopy is a widely used technique for characterizing the structure and dynamics of macromolecules. Often large amounts of NMR data are required to characterize the structure of proteins. To save valuable time and resources on data acquisition, simulated data is useful in the developmental phase, for data analysis, and for comparison with experimental data. However, existing tools for this purpose can be difficult to use, are sometimes specialized for certain types of molecules or spectra, or produce too idealized data. Here we present a fast, flexible and robust tool, VirtualSpectrum, for generating peak lists for most multi-dimensional NMR experiments for both liquid and solid state NMR. It is possible to tune the quality of the generated peak lists to include sources of artifacts from peak overlap, noise and missing signals. VirtualSpectrum uses an analytic expression to represent the spectrum and derive the peak positions, seamlessly handling overlap between signals. We demonstrate our tool by comparing simulated and experimental spectra for different multi-dimensional NMR spectra and analyzing systematically three cases where overlap between peaks is particularly relevant; solid state NMR data, liquid state NMR homonuclear (1)H and (15)N-edited spectra, and 2D/3D heteronuclear correlation spectra of unstructured proteins. We analyze the impact of protein size and secondary structure on peak overlap and on the accuracy of structure determination based on data of different qualities simulated by VirtualSpectrum.
authors.affiliation: Department of Chemistry, Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark, jtn@chem.au.dk.
authors.forename: Jakob Toudahl
authors.initials: JT
authors.lastname: Nielsen
authors.forename: Niels Chr
authors.initials: NC
authors.lastname: Nielsen
mesh_terms: D003198:Computer Simulation; D064267:Intrinsically Disordered Proteins; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D064267:Intrinsically Disordered Proteins; D011506:Proteins