 Upon completion of his Ph.D., Ortiz joined Prof. Jeffrey Skolnick's group at the Department of Molecular Biology at the Scripps Research Institute in United States (1996–2000).There he significantly contributed to the development of MONSTER, at the time one of the most successful Monte Carlo algorithms for predicting protein structure in the absence of a template, as assessed in the Critical Assessment of Techniques for Protein Structure Prediction (CASP), a contest for which he would soon be acting as an advisor.