 In modeling protein structure as of CASP6 , Robetta first searches for structural homologs using BLAST , PSI @-@ BLAST , and 3D @-@ Jury , then parses the target sequence into its individual domains , or independently folding units of proteins , by matching the sequence to structural families in the Pfam database . Domains with structural homologs then follow a " template @-@ based model " ( i.e. , homology modeling ) protocol . Here , the Baker laboratory 's in @-@ house alignment program , K * sync , produces a group of sequence homologs , and each of these is modeled by the Rosetta de novo method to produce a decoy ( possible structure ) . The final structure prediction is selected by taking the lowest energy model as determined by a low @-@ resolution Rosetta energy function . For domains that have no detected structural homologs , a de novo protocol is followed in which the lowest energy model from a set of generated decoys is selected as the final prediction . These domain predictions are then connected together to investigate inter @-@ domain , tertiary @-@ level interactions within the protein . Finally , side @-@ chain contributions are modeled using a protocol for Monte Carlo conformational search . 
