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O'Mara, Patrick

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O'Mara

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O'Mara, Patrick

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    EpiProt: A Java Application Combining Protein Information With Epitope Prediction Software
    (2016-11-10) O'Mara, Patrick; Agostino, Michael; Denkin, Steven
    EpiProt is a bioinformatics suite designed to help users determine antigenic regions within proteins for the production of antibodies. It combines seven epitope prediction programs (five from the Immune Epitope Database, ABCPred and BcePred) with protein annotation information giving users a comprehensive view of a protein targeted for antigen design. The user can perform BLAST searches using UniProtJAPI to find similar proteins to perform pairwise and multiple sequence alignments using ClustalW, Clustal Omega, MUSCLE, T-coffee, or MAFFT. The resulting alignment is shown in a display where the user can annotate the alignments with predicted epitope regions, post-translational modifications (from PhophoSitePlus and UniProt), subcellular location (UniProt), protein processing (UniProt), secondary structure (from SIFTS/PDB) and predicted secondary structure (PsiPred and JPred). Built using Java 8, EpiProt uses Java Swing to create the graphical user interface. EpiProt is designed with a model-view-presenter (MVP) architecture pattern requiring an internet connection to run and collect data via Representational State Transfer (RESTful) for viewing.