Software Purpose Link DFIRE Protein conformation free energy score http://sparks.informatics.iupui.edu/hzhou/dfire.html DSSP Secondary structure assignment http://swift.cmbi.ru.nl/gv/dssp fr-TM-align Protein structural alignment http://cssb.biology.gatech.edu/fr-tm-align Jackal Protein structure modeling http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal MaxCluster Protein structure comparison and clustering http://www.sbg.bio.ic.ac.uk/~maxcluster/index.html Modeller Protein structure modeling http://salilab.org/modeller Pulchra All-atom reconstruction from the backbone Cα atoms http://cssb.biology.gatech.edu/PULCHRA Stride Secondary structure assignment http://webclu.bio.wzw.tum.de/stride TASSER-Lite Protein structure modeling http://cssb.biology.gatech.edu/TASSER-Lite TM-score Protein structure similarity measure http://zhanglab.ccmb.med.umich.edu/TM-score

Table 2: Structure-based tools. Components of the eThread pipeline for protein structure modeling and analysis.