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Performs similarity-based docking by finding templates from the database of experimentally determined structures and building models using energy-based optimization that allows for structural flexibility. GalaxyPepDock can therefore effectively model the structural differences between the template and target protein–peptide complexes. The performance of GalaxyPepDock is superior to those of the other currently available web servers when tested on the PeptiDB set and on recently released complex structures. When tested on the CAPRI target 67, GalaxyPepDock generates models that are more accurate than the best server models submitted during the CAPRI blind prediction experiment.

EPI-Peptide Designer

A computational method to generate libraries of peptide ligands or paratope mimetics based on the epitope-paratope interaction (EPI) patterns and on a target epitope input sequence. EPI-Peptide Designer uses a set of Ab-Ag complex structures from the Protein Data Bank (PDB) and the Blue Star STING server and STING DB containing hundreds of interaction descriptors reported in residue by residue fashion to compute the Bayesian probabilities of molecular interactions between epitope and paratope. EPI-Peptide Designer generates peptide binder sequences based on the epitope sequence entered by the user and the patterns extracted from the Ab-Ag interfaces. This tool should enable the development of a new generation of synthetic interacting peptides that could be very useful in the biosensor, diagnostic and therapeutic fields.