Protein & Binder Design
Computational approaches to de novo protein and antibody design using diffusion models, structure prediction, and generative AI. I participate in open binder design competitions where designs are experimentally validated in the wet lab.
For my antibody design research (benchmarks, tools, analysis), see the Antibody Research hub.
Competitions
Open binder design challenges with experimental validation. Designs are synthesized and tested in the lab by the competition organizers.
Resources & Reading
A curated collection of the best writing on antibody engineering, protein design, and computational biology. Useful starting points whether you're new to the field or deep in the weeds.
Primers & Overviews
Accessible overview of how AI is reshaping antibody discovery, from structure prediction to generative design.
The full journey of antibody development from biology to manufacturing, written for a general technical audience.
Comprehensive technical review of every major AI antibody design platform and method as of 2025.
Owl Posting — Antibody Engineering Series
Antibody structure basics (Fab, CDRs, variable regions), key datasets like OAS, and a walkthrough of major ML models in the field.
What's broken about traditional antibodies, and three alternatives: scFvs, nanobodies (VHH), and antibody mimetics.
Deep-dive on Nabla Bio's approach: engineer the target presentation, not just the antibody, to get better binders.
Escalante Bio — Practical Protein Design
A frank take on the current state of computational binder design—the tools work, and the barrier to entry is lower than you think.
How a minimal pipeline won the computational round of the same Nipah competition I participated in.
The experimental results: which designs actually bound, and what that tells us about the in silico–to–wet lab gap.
On mosaic, Escalante's JAX-based PSSM optimization tool for protein design, and coaxing diffusion models into novel folds.
Software abstractions for bridging the gap between computational design and automated wet-lab execution.
Thinking about biological experiments through the lens of computational complexity—wall-clock time matters.
My Antibody Research
Analysis, benchmarks, and tools for de novo antibody design.