De novo prediction of protein structures, the prediction of structures from amino acid sequences which are not similar to those of hitherto resolved structures, has been one of the major challenges in molecular biophysics. In this paper, we develop a new method of de novo prediction, which combines the fragment assembly method and the simulation of physical folding process: structures which have consistently assembled fragments are dynamically searched by Langevin molecular dynamics of conformational change. The bench-marking test shows that the prediction is improved when the candidate structures are cross-checked by an empirically derived score function. (C) 2008 Elsevier Inc. All rights reserved.