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Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinformatics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-based modeling, which combines computational tools recently developed in our laboratory: the database of protein domain structures (BDDB) with one dimensional and three dimensional threading applications. The protocol was tested during a CASP11 experiment.