EpiProt: A Java Application Combining Protein Information With Epitope Prediction Software The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation O'Mara, Patrick. 2016. EpiProt: A Java Application Combining Protein Information With Epitope Prediction Software. Master's thesis, Harvard Extension School. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:33797405 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA EpiProt: A Java Application Combining Protein Information with Epitope Prediction Software Patrick O’Mara A Thesis in the Field of Biotechnology for the Degree of Master of Liberal Arts in Extension Studies. Harvard University November 2016 Abstract 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. Table of Contents List of Tables ................................................................................................................... viii List of Figures .................................................................................................................... ix I. Introduction .....................................................................................................................1! Antibodies and Antigens ..........................................................................................2! Epitopes ....................................................................................................................2! In Vivo Generation of Antibodies ............................................................................3! Manufacturing Antibodies for Applications ............................................................4! Antigen Design Principles .......................................................................................7! Accessibility .................................................................................................8! Immunogenicity ...........................................................................................8! Specificity ....................................................................................................9! Antigen Design Process .........................................................................................10! Intra-species Alignment .............................................................................10! Inter-species Alignment .............................................................................11! Isoform Alignment .....................................................................................11! Protein Annotation .....................................................................................12! Protein structure .............................................................................12! Topology and protein interaction information ...............................14! Post-translational modifications and mutation sites ......................14! Protein processing ..........................................................................15! iv General guidelines .........................................................................16! Antigen Design Summary ..........................................................................16! Epitope Prediction Sources ....................................................................................17! Similar Approaches and Deficiencies ....................................................................17! MacVector ..................................................................................................18! Jalview .......................................................................................................19! AbDesigner ................................................................................................21! Ig-score ..........................................................................................23! Uniqueness .....................................................................................23! Conservation ..................................................................................23! II. Software Design ...........................................................................................................25! Development Software ...........................................................................................25! Third-Party Software .............................................................................................25! PsiPred 3.5 .................................................................................................26! JPred 1.5 .....................................................................................................29! JABAWS 2.1.0 ..........................................................................................29! III. Software Architecture .................................................................................................30! View .......................................................................................................................32! General Display .........................................................................................32! Menu Bars ......................................................................................33! BLAST panel .................................................................................34! Header Pane ...................................................................................34! v Editor Pane .....................................................................................35! Purpose .......................................................................................................35! Presenter .................................................................................................................37! Model .....................................................................................................................37! Data Access Objects ..................................................................................39! Not MVP: Protein.java...............................................................................40! The Services ...............................................................................................41! UniprotService.java .......................................................................41! UniprotBlastService.java ...............................................................42! PsiPredService.java ........................................................................42! JPredService.java ...........................................................................42! SiftService.java ..............................................................................43! PhosphoSitePlus.java .....................................................................43! IedbEpitopePredictionService.java ................................................43! BcePredPredictionService.java ......................................................44! ABCPredService.java ....................................................................46! JabawsService.java ........................................................................48! IV. Summary and Conclusion ...........................................................................................50! Proposed vs. Actual Program .................................................................................50! Future Considerations ............................................................................................51! Summary ................................................................................................................52! Appendix ............................................................................................................................55! vi Additional Tables ...................................................................................................55! Source Code ...........................................................................................................59! Bibliography ....................................................................................................................423! vii List of Tables Table 1. Summary of the epitope prediction programs available in EpiProt