Topic
Bioinformatics
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 Bioinformatics How to Predict B-Cell Epitopes with BepiPred and ABCpred: A Step-by-Step Guide Run BepiPred and ABCpred on the same antigen, read per-residue scores against the threshold, and keep only consensus peptides. Start with this… Ragini Mishra 15 min read Bioinformatics How to Install GROMACS: A Beginner’s Guide for Windows, Linux and Google Colab Install GROMACS the right way on Linux, Windows (WSL2), or free Google Colab. Follow the exact commands and run your first gmx… Dr. Abdul Rajjak Shaikh 10 min read Updated Bioinformatics What Is Sequence Alignment? A Beginner’s Guide for Bioinformatics Learn what sequence alignment is, how pairwise and multiple alignment work, how scoring and gaps are handled, and the beginner tools used… Dr. Abdul Rajjak Shaikh 8 min read Updated Bioinformatics What Is a Protein Binding Site? A Beginner’s Guide Learn about protein binding sites, their types (active, allosteric), and how computational tools identify them for drug design and molecular modeling. Dr. Abdul Rajjak Shaikh 8 min read Updated Bioinformatics PCR Explained: Principles, Steps & Troubleshooting Guide (2025-26) PCR is the workhorse of molecular biology. This beginner-friendly guide breaks down the science, the steps, and how to fix common errors… Dr. Abdul Rajjak Shaikh 12 min read Updated