BDG Lifesciences

BDG Lifesciences Official page of BDG Lifesciences (OPC) Private Limited, India. Expertise in services of Bioinformat

Day 10. Ten days ago, it was a FASTA file.Today, it is a codon-optimised mRNA sequence ready for human expression.That i...
11/06/2026

Day 10. Ten days ago, it was a FASTA file.

Today, it is a codon-optimised mRNA sequence ready for human expression.

That is the full length of the journey this workshop covers.

Somewhere between those two points: forty proteins retrieved and filtered to twenty-six. Antigenicity scored. Allergenicity screened. B-cell epitopes mapped from sequence. Conformational epitopes mapped from structure. T-cell peptides predicted across MHC Class I and Class II. CTL epitopes ranked by percentile. Population coverage calculated against real human HLA diversity. Constructs assembled, linker by linker. Models folded and validated against a Ramachandran threshold. A crystal structure of TLR10 pulled from a structural archive. A docking job submitted, processed, and returned with a binding energy score of −144.95.

And then — the mRNA side. Signal peptides. Adjuvant sequences. Targeting domains. UTR elements. A poly(A) tail. An entirely parallel pipeline, assembled and validated in the final two days, ending with a nucleotide sequence that a synthesis facility could, in principle, make real.

Ten days. Two vaccine platforms. One computational methodology that belongs to every participant who completed it.

The next batch is coming. If you were watching from the outside — this is the one to be inside for. Join the next one from here 🌐 https://bdglifesciences.com/event/insilico-protein-mrna-vaccine-design

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

"I don't know where to start with bioinformatics" is the most common thing we hear from students and researchers. 😅So we...
10/06/2026

"I don't know where to start with bioinformatics" is the most common thing we hear from students and researchers. 😅

So we built a 7-day programme that starts at day one — literally. Databases, sequence analysis, protein structure, phylogenetics, genome browsers — all hands-on, all with a live trainer.

Dr. Sharvari Kulkarni walks you through every tool, every step, on your own system.

June 18–24. Registration link in bio 👆 🌐 or https://bdglifesciences.com/event/bioinformatics

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

Day 5 of 10. Simulation analysed. Results: excellent. ✅Running a simulation is one thing. Knowing whether it worked — an...
10/06/2026

Day 5 of 10. Simulation analysed. Results: excellent. ✅

Running a simulation is one thing. Knowing whether it worked — and being able to prove it in a publication — is something else entirely.

Today our participants generated everything a journal reviewer expects to see from an MD simulation run. Energy graphs from the log file: potential energy dropping to equilibrium and holding. Temperature stable at 310 K throughout. RMSD for the sphere simulation came in at ~1.05 Å. The accepted threshold is 4.8 Å. That result is not just acceptable — it is clean.

They also generated publication-quality protein images in VMD. Tube rendering. BGR colour scale. Blue for the rigid regions. Green for moderate movement. Red for the residues with the highest atomic fluctuation. That image is submission-ready.

Every graph, every plot, every image — produced from trajectory data they ran themselves, on their own machines, four days into a ten-day workshop.

Box simulation analysis is homework. Day 6 is Linux installation and GROMACS.

The second half of this workshop is about to begin.

If you were not in this batch, watch for the next announcement. By Day 5, participants are producing and interpreting real MD simulation data independently.

📍 Online | Certificate Programme
🔬 NAMD · VMD · GROMACS · Linux · Windows

Join the next one from here 🌐 https://bdglifesciences.com/event/md-simulation

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

We designed thousands of sgRNAs. Off-target mismatch tolerances we've run. Cas9 structures we've interpreted. And every ...
10/06/2026

We designed thousands of sgRNAs. Off-target mismatch tolerances we've run. Cas9 structures we've interpreted. And every bit of it took years of building the right workflows. 🧬

Now we're teaching it — all of it — in 10 days.

BDG LifeSciences' CRISPR & Gene Therapy Workshop kicks off June 16. If you're in molecular biology, genomics, or biomedical research and you've been waiting for the right programme, this is it. Swipe for the full curriculum 👉

Link in bio to register 🌐 or https://bdglifesciences.com/event/crispr-gene-therapy-online-workshop

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

Day 9. Two pipelines. One session.For eight days, participants worked a single pipeline — protein vaccine design, from s...
09/06/2026

Day 9. Two pipelines. One session.

For eight days, participants worked a single pipeline — protein vaccine design, from sequence retrieval to structure validation. Today, they ran two simultaneously.

Pipeline one: the protein vaccine reached its docking stage. TLR10 — the innate immune receptor that a vaccine antigen must engage to trigger protective signalling — was pulled from the Protein Data Bank as a validated crystal structure. The vaccine construct, modelled and validated on Day 8, was submitted alongside it to HDOCK. The server is now calculating how, and how well, they interact. Results come tomorrow, in the final session.

Pipeline two: a new workflow opened from scratch, this time for mRNA vaccine design against Mycobacterium tuberculosis — one of the oldest and most persistent infectious disease challenges in global health. Twenty protein sequences retrieved. Antigenicity screened. Allergenicity filtered. B-cell and T-cell epitopes mapped across MHC Class I and Class II pathways.

The same steps. The same logic. A different pathogen, a different vaccine platform, and the same immunoinformatics framework underneath it all.

That is the thing about this methodology. Once you understand it, it does not belong to one project. It belongs to you.

One session remains. Docking results. Final constructs. The end of ten days of building something real.

If you missed this batch — you know where to find us for the next one 🌐 https://bdglifesciences.com/event/insilico-protein-mrna-vaccine-design

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

Day 4 of 10. First simulation run. ✅The blinking cursor in the command prompt is one of those moments in computational r...
09/06/2026

Day 4 of 10. First simulation run. ✅

The blinking cursor in the command prompt is one of those moments in computational research that stays with you. Your system is solving Newton's equations of motion for thousands of atoms, one femtosecond at a time.

Today our participants saw it for the first time — and waited for it to finish.

Sphere simulation: done. Box simulation: done. Eleven output files generated for each. The log file is sitting in the folder, recording every time step of the trajectory, ready for analysis.

Not everything ran cleanly on the first attempt. Path errors. A missing DLL file. Nested folder structures in the wrong place. Every single one was diagnosed, traced to its exact cause, and fixed. That is not a detour — that is the skill.

Three days of preparation. One command. The simulation ran.

Day 5 is output analysis: RMSD, RMSF, SASA, radius of gyration, hydrogen bond plots. The data is ready. Now comes the interpretation.

If this is the kind of training you want, the next workshop will be announced soon. Four days in, participants are already running production MD simulations on their own machines.

📍 Online | Certificate Programme
🔬 NAMD · VMD · GROMACS · Linux · Windows

Join the next one from here 🌐 https://bdglifesciences.com/events/workshop/online-workshops

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

Day 8. The sequences got their shape.For seven days, the vaccine constructs existed as letters on a screen. Amino acid s...
08/06/2026

Day 8. The sequences got their shape.

For seven days, the vaccine constructs existed as letters on a screen. Amino acid sequences, carefully filtered and assembled — but flat. Dimensionless.

Today that changed.

Participants submitted their vaccine candidate sequences to SWISS-MODEL and watched homology modelling do what it is designed to do — find structurally similar proteins in the world's crystallography archive, use their resolved geometry as a scaffold, and infer the three-dimensional shape of something that has never been crystallised.

Because no one has ever crystallised these constructs before. They were designed here, in this workshop, from scratch.

Once the models were generated, they went straight into validation. MolProbity. Ramachandran plots. Clash scores. Rotamer analysis. Not to produce a number — but to answer a specific question: is this model physically credible enough to trust in a docking simulation?

Models that pass go forward. Models that do not get corrected before anything else happens. That standard is what separates a publishable structural result from a decorative one.

The cartoon-style 3D visualisations generated today? Those go into the research paper. The validation tables? Those go into the dissertation. Two different audiences. Two different formats. Both important.

Two sessions left. The validated structures meet their receptor targets next.

If you are not in this batch — this is the kind of session that cannot be replicated by watching a tutorial. You have to build the sequence to understand why the structure matters. 🌐 Join the next one from here- https://bdglifesciences.com/events/workshop/online-workshops

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

Day 3 of 10. Every file in place. Configuration understood. ✅Today our participants did something most researchers skip ...
08/06/2026

Day 3 of 10. Every file in place. Configuration understood. ✅

Today our participants did something most researchers skip — they read the configuration file before running the simulation.

Every parameter. Every line. Temperature set to 310 K because that is body temperature. Time step at 2 femtoseconds because that is the physical limit before numerical integration breaks down. Restart frequency every 500 steps so that a power cut or a crash does not cost you the entire run.

They also completed water box solvation, visualised both a water sphere and a water box around the same protein in VMD, and organised all six input files into a single folder ready for the simulation engine.

Most people who run MD simulations have never read the configuration file that controls them. Every participant in this workshop has.

Day 4 is the NAMD simulation run, trajectory outputs, and analysis. The 11 output files are about to be generated.

If you were not in this batch, the next workshop will be announced soon. This is the preparation that separates a researcher who runs simulations from one who understands them.

📍 Online | Certificate Programme
🔬 NAMD · VMD · GROMACS · Linux · Windows

Join the next one from here 🌐 https://bdglifesciences.com/events/workshop/online-workshops

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

Day 7. The constructs got their third arm.A vaccine that only triggers antibodies covers one part of the immune system. ...
08/06/2026

Day 7. The constructs got their third arm.

A vaccine that only triggers antibodies covers one part of the immune system. A vaccine that also activates helper T-cells covers a second. But there is a third arm — cytotoxic T lymphocytes — the immune system's targeted killers. The cells that find infected cells and eliminate them directly.

Today, participants predicted CTL epitopes. The specific peptide sequences that, once presented by MHC Class I molecules, instruct cytotoxic T-cells to act.

Two prediction tools. The same 14 proteins. Results ranked by percentile, highest-confidence sequences selected, PDFs saved and organised.

Then came the harder part — rebuilding the vaccine constructs with all three arms included. B-cell epitopes for antibody responses. MHC Class II peptides for helper T-cells. MHC Class I and CTL epitopes for cytotoxic responses. Three linker types — GPGPG, AAY, EAAK — connecting them in a sequence architecture that preserves the immunological function of every component.

14 novel protein sequences. Each one a more complete representation of a protective immune response than anything assembled earlier in this workshop.

Three days remain. Structural prediction and docking are next.

The full picture is almost built. If you want to build it yourself — watch for the next batch. 🌐 Join the next one from here https://bdglifesciences.com/events/workshop/online-workshops

📲 Join our WhatsApp Channel for updates on Jobs, News, Training, Workshops & Research Projects: https://whatsapp.com/channel/0029VagPqwB6GcG7TZzIPi2R

Day 2 of 10. Files built. System solvated. ✅Before any MD simulation runs, you need four things built correctly: the PDB...
07/06/2026

Day 2 of 10. Files built. System solvated. ✅

Before any MD simulation runs, you need four things built correctly: the PDB coordinate file, the PSF topology file, the force field parameters, and the configuration file. Get one wrong and nothing runs.

Today our participants built all of them — inside VMD's TK console, command by command. They cleaned the protein structure, generated PSF topology using CHARMM27 force field parameters, and surrounded ubiquitin with a water sphere that mimics the physiological environment a protein actually lives in.

The final visualisation said it all: ubiquitin in blue, sitting at the centre of a red water sphere. That is what a properly prepared MD simulation input looks like.

Day 3 is the configuration file and the first NAMD run. It gets more demanding from here.

If you were not in this batch, the next workshop will be announced soon. You will want to be in it before the seats fill.

📍 Online | Certificate Programme
🔬 NAMD · VMD · GROMACS · Linux · Windows

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