Topic
Bioinformatics
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 Bioinformatics How to Check Epitope Allergenicity, Toxicity and Antigenicity: VaxiJen, AllerTOP and ToxinPred Screen your epitope shortlist properly: which server to run first, which threshold to set, and what to do with a borderline score.… Ragini Mishra 14 min read Bioinformatics How to Design a Multi-Epitope Vaccine Construct: Linkers, Adjuvant and Order Join your shortlisted epitopes into one designed protein: which linker goes where, why order matters, and how to validate the sequence. Build… Ragini Mishra 14 min read Bioinformatics How to Predict T-Cell Epitopes and MHC Binding with NetMHCpan and IEDB Pick an HLA panel, set the right peptide length, and filter on percentile rank. Turn thousands of NetMHCpan rows into a defensible… Ragini Mishra 17 min read Bioinformatics How to Download a Protein Structure from the RCSB PDB and Read the File Find, download, and actually read a protein structure from the RCSB PDB before you dock or run MD. Start your modelling workflow… Dr. Abdul Rajjak Shaikh 9 min read Updated