Topic
Bioinformatics
Bioinformatics How to Predict Conformational B-Cell Epitopes Run ElliPro, DiscoTope 3.0 and SEPPA 3.0 on a structure, read their scores correctly, and avoid the residue-numbering trap. Ragini Mishra 17 min read Bioinformatics How to Predict IFN-gamma, IL-4 and IL-10 Inducing Epitopes Screen your shortlisted MHC class II binders for IFN-gamma, IL-4 and IL-10 induction, and learn when a high score is a reason… Ragini Mishra 15 min read Bioinformatics Epitope Conservancy Analysis: A Step-by-Step Guide Run an epitope conservancy analysis across strains and variants, pick a defensible identity threshold, and learn the inverse host-proteome test. Ragini Mishra 16 min read Bioinformatics Multi-Epitope Vaccine Structure: Model, Refine, Validate Model a vaccine construct with no template, read the low pLDDT at your linkers correctly, refine it, and validate it before you… Ragini Mishra 13 min read Bioinformatics How to Select Target Antigens for Reverse Vaccinology Start a vaccine design project right. Five filters, in order, that cut a whole proteome down to the proteins worth predicting epitopes… Ragini Mishra 11 min read Bioinformatics ProtParam for a Vaccine Construct: Reading Every Number Run ProtParam on your multi-epitope construct and learn what each number means, which cutoff is real, and what to change when a… Ragini Mishra 16 min read Bioinformatics How to Run an IEDB Population Coverage Analysis for Your Epitope Set Run the IEDB Population Coverage tool step by step, format the input correctly, read PC90 properly, and fix thin coverage in South… Ragini Mishra 13 min read Bioinformatics How to Codon Optimize a Vaccine Construct for E. coli Expression: Codon Usage, CAI and Restriction Sites Learn how to codon optimize a multi-epitope vaccine construct for E. coli: reverse translation, CAI, GC3 and the restriction-site check before you… Ragini Mishra 15 min read Bioinformatics How to Get the Right Protein Sequence from UniProt for Modelling (Canonical Isoform, Signal Peptide and Residue Numbering) Pick a reviewed Swiss-Prot entry, take the canonical isoform, cut the signal peptide, and check the PDB offset before you model. Follow… Dr. Abdul Rajjak Shaikh 13 min read Bioinformatics How to Dock a Multi-Epitope Vaccine Construct with TLR4: ClusPro, HDOCK and HADDOCK Compared Dock a screened vaccine construct against TLR4 the way a reviewer reads it: pick the PDB entry, prep the files, compare three… Ragini Mishra 16 min read