Software Purpose Link
DFIRE Protein conformation free energy score
DSSP Secondary structure assignment
fr-TM-align Protein structural alignment
Jackal Protein structure modeling
MaxCluster Protein structure comparison and clustering
Modeller Protein structure modeling
Pulchra All-atom reconstruction from the backbone Cα atoms
Stride Secondary structure assignment
TASSER-Lite Protein structure modeling
TM-score Protein structure similarity measure
Table 2: Structure-based tools. Components of the eThread pipeline for protein structure modeling and analysis.