Modeller
Software from Andrej Sali’s group for homology or comparative modelling of protein three dimensional structures
Sali A, Blundell TL, J Mol Biol (1993) 234 779-815 pdf

Phenix
Software for automated determination of macromolecular structures using X-ray crystallography and other methods
Acta Cryst (2010) D66 213-221 pdf