TL;DR
Technical triage for alternative pseudotyping glycoproteins against VSV-G / Cocal-G risk anchors.
Use it / Skip it
The page ranks candidate envelopes by sequence similarity, equivalent-position mapping, and technical risk so wet-lab and IP review can focus on a smaller set.
Use when
A lentiviral envelope program needs alternatives or a 354-position risk discussion must be made reproducible.
Don't use for
Do not use it as legal advice, freedom-to-operate conclusion, or final packaging protocol.
Inputs
- Candidate FASTA
- One or more candidate glycoprotein sequences.
- References
- VSV-G and Cocal-G references; defaults can be fetched where configured.
- Optional UniProt query
- Exploratory recall for candidate sequence collection.
Outputs
- assessments.csv
- Ranked spreadsheet with identity, equivalent residue, risk band, score, and reasons.
- assessments.json
- Machine-readable full result.
- manifest.json/report
- Input summary and technical-triage caveats.
Walkthrough
1. Start with a curated FASTA when possible
Start with a curated FASTA when possible. Broad search results often need manual cleanup.
2. Run the assessment from the web page or CLI and wait for persisted artifacts
Run the assessment from the web page or CLI and wait for persisted artifacts.
3. Read VSV-G identity and 354-equivalent mapping together
Read VSV-G identity and 354-equivalent mapping together.
4. Shortlist candidates for structural review, packaging assay, and IP counsel review
Shortlist candidates for structural review, packaging assay, and IP counsel review.
Under the hood
- Core implementation lives under pipeline/g_protein_design_around.
- Biopython PairwiseAligner supports identity and reference-position mapping.
- The web surface persists jobs and exposes CSV/JSON/report artifacts.
Worked example
Pitfalls
- Below 85% identity is not automatically safe.
- Very low identity may be legally distant but biologically unusable.
- Alignment-based equivalent-position mapping needs manual review for distant homologs.