recently published method: PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues (http://osddlinux.osdd.net/raghava/pepstrmod/)
article link : http://www.biologydirect.com/content/10/1/73
In this article the PEPstrMOD is compared with ab initio models and performance of PEPstrMOD is far better than ab initio models. Therefore it is advisable to use peptide tertiary structure prediction method rather than ab initio models.