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• 22:09, 29 September 2026 Carol talk contribs created page Exercise:AllergenicityPrediction ans (Created page with "== Answers == === Get the Data and Filter It === *'''Q1A:''' What would be your first approach to determine whether brown algae contain potential allergens? Find one database containing experimentally characterized allergens. Consider what biological information you would search for and what properties of the proteins might provide evidence of allergenic potential. '''Answer:''' *'''Q1B:''' Now imagine that no computational predictor specifically designed for allerg...")
• 18:35, 29 September 2026 Carol talk contribs created page Exercise:AllergenicityPrediction (Created page with "Exercise written by Carolina Barra Quaglia == Introduction == Immunopeptidomics experiments can identify thousands of peptides presented on the cell surface by MHC molecules. However, because an individual can express several different HLA alleles, it is often not immediately clear which HLA molecule is responsible for presenting each peptide. In addition, immunopeptidomics datasets may contain co-purified peptides that are not true MHC ligands. In this exercise, we w...")
• 22:10, 22 September 2026 Carol talk contribs created page File:MHCMotifDecon rank2.png
• 22:10, 22 September 2026 Carol talk contribs uploaded File:MHCMotifDecon rank2.png
• 22:09, 22 September 2026 Carol talk contribs created page File:MHCMotifDecon rank20 extendedHLA.png
• 22:09, 22 September 2026 Carol talk contribs uploaded File:MHCMotifDecon rank20 extendedHLA.png
• 22:09, 22 September 2026 Carol talk contribs created page File:MHCMotifDecon rank20.png
• 22:09, 22 September 2026 Carol talk contribs uploaded File:MHCMotifDecon rank20.png
• 19:57, 22 September 2026 Carol talk contribs created page Exercise:AntigenProcessing ans (Created page with " *'''Q1: How many epitopes do you find with the initial filter?''' *'''Q2: Do you agree with calling these peptides epitopes? Why?''' Now refine your search by including only '''mass-spectrometry assays''' on '''HLA-DR restriction alleles'''. From the '''References''' tab, select the publication from the ''Journal of Proteome Research'' from 2017 by Wang et al. *'''Q3: How many eluted ligands did they find in this study?''' Under the '''Assays''' tab, select '''MHC...")
• 17:29, 22 September 2026 Carol talk contribs created page Exercise:AntigenProcessing (Created page with "== MHC Motif Deconvolution == Immunopeptidomics is currently used in several biomedical applications, including neo-epitope discovery in oncology, protein-drug immunogenicity assessment, as well as next-generation vaccine development. Immunopeptidome data are highly complex given the expression of multiple HLA alleles on the cell membrane and the presence of co-immunoprecipitated contaminants, which is an inherent drawback of the immunopeptidomic workflow. To resolve t...")
• 11:47, 6 August 2026 Carol talk contribs created page 22145 Immunological Bioinformatics Course Programme Fall 2026 (Created page with "== General information == === Where and when === Wednesday from 9 to 12 in '''building 208, holdlokale 3/065''', starting on '''Wednesday, Sep 3 at 9:00'''. Classess will start at 9am unless specified. The first hour of the course will be dedicated to course-preparation. Including some videos or paper reading material === Teachers === * [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible. *...")
• 19:30, 4 November 2025 Carol talk contribs created page Bcell Epitope prediction answers (Created page with "'''B-cell epitope prediction — Why do some flu vaccines miss? Influenza A hemagglutinin (HA) has two very different antibody targets: the variable head and the conserved stem. Head-binding antibodies often lose potency as the virus drifts; stem-binding broadly neutralizing antibodies (bnAbs) can resist drift. Can standard sequence-based and structure-based B-cell epitope predictors tell these stories apart? '''Part A, Get your bearings in PyMOL (find the ground truth...")
• 13:25, 24 October 2025 Carol talk contribs created page Bcell Epitope prediction (Created page with "We want to look for epitopes on the HIV GP120 protein. We will use both sequence-based and structure-based methods. Input data. Go to the pdb homepage and look for the pdb entry 4LSP. It is GP120 complexed with a broadly neutralizing antibody. These antibodies are extremely powerful, since they are effective against many different strains. Q1: Download both the structure (pdb) and the sequence (fasta) of the proteins in this entry. Which proteins are in chain G, L and...")
• 13:12, 24 October 2025 Carol talk contribs created page Epitope prediction (Created page with "'''B-cell epitope prediction exercise''' VEGF (vascular endothelial growth factor) is a target in cancer therapies, being the protein responsible for vascularization of tumoral tissue. The murine anti-VEGF antibody has been proved to be effective in blocking VEGF, but it is immunogenic. The Bevacizumab is the commercial, humanized version of the antibody. Let’s reproduce its humanization. Anti-VEGF Humanization The sequence of the murine antibody is: >Light chai...")
• 17:12, 20 October 2025 Carol talk contribs created page Antibody Modelling (Created page with "'''Humanization of the anti-VEGF antibody''' VEGF (vascular endothelial growth factor) is a target in cancer therapies, being the protein responsible for vascularization of tumoral tissue. The murine anti-VEGF antibody has been proved to be effective in blocking VEGF, but it is immunogenic. The Bevacizumab is the commercial, humanized version of the antibody. Let’s reproduce its humanization. Anti-VEGF Humanization The sequence of the murine antibody is: >Light c...")
• 13:10, 7 August 2025 Carol talk contribs created page 22145 Immunological Bioinformatics Course Programme Fall 2025 (Created page with "== General information == === Where and when === Wednesday from 8 to 12 in '''building 208, holdlokale 3/065''', starting on '''Wednesday, Sep 4 at 8:00'''. === Teachers === * [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible. * [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course responsible. === Teaching assistant === * [https://w...")
• 20:02, 25 August 2024 Carol talk contribs created page 22145 Immunological Bioinformatics Course Programme Fall 2024 (Created page with "== General information == === Where and when === Lectures and exercises will take place every Wednesday morning from 8 to 12 in '''Holdlokale 3/065, building 208''', starting on '''Wednesday, Sep 4 at 8:00'''. === Teachers === * [https://www.dtu.dk/Person/cwis?id=142840&entity=profile Carolina Barra Quaglia] — Associate professor, course responsible. * [https://www.dtu.dk/person/morten-nielsen?id=5973&entity=profile Morten Nielsen] — Professor, course...")