Modules for reliable 3D structure generation of polyphenolic compounds have been developed. The 1H-NMR chemical shifts, 1H-1H couplings (including strong coupling effects), spectra simulation at 600 Hz, and spectra annotation have been fully automated. The predictions have been performed for four frequently used deuterated solvents as methanol, acetonitrile, chloroform, and DMSO. A database and user interface have been designed and implemented. The visualization modules include interactive views of the simulated spectra and the 3D structures. The hydrogen and carbon atom labelling (“atom numbers”) is according to literature, making comparison between the server and published data very easy. The web server with the NMR data and structures will be made available in the Q1 of 2011. The first release of the database will contain about 6000 polyphenolic compounds. In addition to metabolite identification, metabolite quantification can be performed by fitting 1H-NMR spectra of complex biological samples. Building a library of high quality 1H-NMR spectra of standard compounds measured at strictly defined experimental conditions has been started. Our aim is to be able to quantify simultaneously and in an automated manner up to 50 metabolites.