Coralyne is an alkaloid DNA-binding drug. Unlike other DNA-binding drugs, coralyne is known to strongly bind poly(dA) and to form a complex which has a binding constant greater than that of a coralyne to B-DNA. Despite its strong affinity towards poly(dA), the structure of coralyne-poly(dA) complex remains elusive. Hud and co-workers show that the poly(dA) in the complex forms anti-parallel duplexes, however their attempts at determining an NMR structure have been unsuccessful. Inspired by their discovery, we attempted to predict 3D structure of the complex by using molecular dynamics simulations. Introducing some reasonable assumptions that include hydrogen bond base-pairing between the two poly(dA) strands, we could construct 36 tentative poly(dA) anti-parallel duplexes. After short restrained molecular dynamics simulations, only six of them were observed to maintain structural integrity. Coralyne molecules were docked into the six duplexes with various orientations. 103 tentative complex structures were built and simulated. Their energetic and structural stabilities were ranked by comparing binding energies calculated using the MM-PBSA method, occupancies of hydrogen bonds between base pairs, and orientations of the inserted coralyne molecules. Groove binding models were readily discarded because of their low binding energies, and thus only intercalation models were investigated further. Interestingly, it was observed that some of the models converged into the same structures. After removing the overlapped structures, the most promising structures were selected for each of the six types of poly(dA) duplexes based on the rank. After performing several nano-seconds of extended simulations, it was confirmed that some of the selected structures generally rank higher than the others. The two best structures were isolated and they showed energetic and structural stability over a long period (> 50 ns). Their high binding energies support the possibility that they could represent real structures of the coralyne-poly(dA) complex.