P. Pliego-Pastrana and M. D. Carbajal-Tinoco. (2005) Polypeptide foldings obtained with effective pair potentials. The Journal of Chemical Physics 122, 244908.
We present a model of protein folding which is based on a potential function that describes the effective interaction between two amino acids (alanines, in this case). Our model is consistent with the formation of two important secondary structures, namely, an ?-helix and a ?-ladder. In each case, we estimate the density of states using a random walk in energy space. This function allows the direct calculation of certain thermodynamic properties. By means of the configurational temperature, we also verify that the obtained polypeptides are in their native state.