 A few years later, he developed, in collaboration with Bin Qian and David Baker, an original and imaginative framework for assisting homology-based modelling of protein structures making use of both empirical knowledge of protein structure evolution and equilibrium dynamics.In 2000 Ortiz moved to New York City and started to work in Mount Sinai School of Medicine, establishing his own researching group on genomics.During this period he developed MAMMOTH, a program that is now consolidated as one of the references in the field of protein structure alignment.