A compound is identified by matching its proton and/or carbon NMR spectra to NIH PubChem molecular structures. The matching process involves analyzing 1D proton, 1D carbon, DEPT, and/or HSQC spectra, and comparing the number of NMR resonances, detected proton and carbon shifts, likely number of methyl- and methoxy-groups, and an optionally specified molecular formula to predicted proton and carbon shifts of PubChem structures. A structure verification module rates the consistency between experimental spectral analysis results and a proposed structure (not limited to PubChem structures) and assigns observed shifts to the proposed structure. The spectral analysis, structure identification, and structure verification are largely automated in a software package and can be performed in minutes.