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List of some of the Applications using the package

Align Pairwise protein sequence alignment and analysis server
Ring Residue interaction network generation method for Cytoscape
TAP Validate the local torsion angles for protein structures
QMEAN Protein model quality estimation based on a comprehensive evaluation
Homer Homology Modeling server, automatic template selection
LOBO Loop modelling server for protein structures
FRST Protein model quality estimation method based on energy evaluation