We present a new method for modeling the overtone structures of musical instruments that uses an overtone corpus generated using a MIDI synthesizer. Since multipitch estimation requires a joint estimation of F0's and their overtone structures, one of the most important problems is the overtone structure modeling. Latent harmonic allocation (LHA), a promising multipitch estimation method, is difficult to use for various applications because it requires appropriate prior distributions of the overtone structures, which cannot be determined from statistical evidence. Our method uses an overtone corpus to avoid the problem of setting prior distributions and instead restricts the lower and upper bounds of each overtone weight. The bounds are determined from reference signals generated by a MIDI synthesizer. Experimental results demonstrated that the overtone structures were stably and accurately estimated for a wide variety of initial settings.