Holographic QCD predicts that nucleons in QCD may be described by D-branes so called baryon vertices in string theory. The effective theory of the baryon vertices is a matrix quantum mechanics similar to the Dp-Dp+4-brane systems. We study this quantum mechanics and find a similarity with the quark model. By solving our model for small numbers of baryons, we obtain the Gell-Mann-Okubo formula for hyperons, baryon resonances, dibaryon spectra, and a stable Helium like nucleus. In such a way, D-brane dynamics may be understood as nuclear physics.