AAV design on the platform
Select an AAV capsid serotype for a target tissue and optimize the transgene cassette for AAV packaging — the gene-therapy tools of the biologics cluster.
An AAV gene therapy is two design problems in sequence: which capsid delivers your payload to the right tissue, and how to fit that payload inside the vector's tight packaging limit. The platform's AAV tools handle both — one selects a capsid serotype for a target tissue given tropism and pre-existing-immunity data, the other codon-optimizes a transgene cassette and checks it against the ~4.7 kb AAV packaging capacity. Together they are the gene-therapy sibling of the antibody engineering cluster.
Try it
The two AAV tools
aav_capsid_select looks up what the literature reports about AAV serotype tropism for a target tissue. For each serotype it returns the tissues a cited study reports, the qualitative level that study reports, the species or system it was observed in, and the citation — plus reported seroprevalence where a study exists. It does not score, rank or recommend a serotype, and the records come back in alphabetical order.
aav_transgene_optimize takes a transgene sequence and produces a codon-optimized cassette. It reverse-translates the sequence, optimizes codon usage against the human codon table with DNA Chisel, avoids a fixed set of restriction sites, and validates the payload size against the AAV packaging limit.
Neither tool designs a cassette, and neither takes a preference you might expect
aav_capsid_select takes a tissue, optionally one serotype to return in full, and optionally a payload size. There is no species, route_of_administration or neutralizing_antibody_profile input: species is reported per observation from the literature rather than requested, seroprevalence comes from the cited studies, and route is not modelled.
aav_transgene_optimize optimizes the coding sequence only. There is no promoter, polyadenylation or regulatory-element input — those are cassette design choices the backend does not make, so assemble them yourself around the sequence it returns. Codon usage is fixed to Homo sapiens.
Citations
Zulkower V, Rosser S. DNA Chisel, a versatile sequence optimizer. Bioinformatics. 2020;36(16):4508-4509. doi: 10.1093/bioinformatics/btaa558
When to reach for them
Reach for capsid selection when you are:
- Starting an AAV gene-therapy design for a specific tissue (CNS, liver, muscle, retina).
- Comparing capsid serotypes for tissue tropism and immunogenicity.
- Selecting capsids with low seroprevalence in a target patient population.
Reach for transgene optimization when you are:
- Designing an AAV transgene cassette after capsid selection.
- Optimizing codon usage for human expression.
- Fitting a transgene within the AAV packaging capacity.
For a small-molecule or antibody program these are not the tools — see antibody engineering or cell & gene therapy for CAR-based modalities.
How they fit together
The two tools run in order: select the capsid first, then optimize the transgene to fit it. Capsid selection tells you the packaging limit you are designing against; transgene optimization checks your cassette against that limit and reports whether it will package. Both are gene-therapy end steps — they produce a vector design rather than feeding another antibody tool.
How they run
Both AAV tools run as asynchronous GPU jobs on Modal compute. You submit the design parameters, the platform tracks and polls the job, and a result card lands on the canvas when it finishes. Capsid selection typically takes a few minutes; transgene optimization can take longer, since codon optimization is an iterative search.
Read next
AAV quickstart
Select a capsid and optimize a transgene in a few steps.
AAV inputs
Target tissue and serotype for the lookup; protein sequence and payload limit for optimization.
AAV outputs
Cited tropism reports per serotype, and the optimized cassette with packaging feasibility.
Antibody engineering
The antibody sibling of the biologics cluster.
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How developability results compare to the bench
What a computed developability flag has been shown to agree with experimentally, and why a sequence-motif flag is not a measured degradation rate.
AAV inputs and parameters
Target tissue, serotype and payload limit for the literature lookup; a protein sequence for the optimizer. No species, route or promoter parameter exists.