Antibody sequence infilling and CDR diversification
Практический сценарий
Нужно разнообразить CDR или infill span без antigen structure.
Вход
- optional sequence context
- span mask
- species/chain tokens
Pipeline diagram
Infilling generation
→Likelihood filter
→Pairing / structure / developability
→Assays
Mermaid diagram
flowchart TD
A[Sequence context + span mask] --> B[IgLM infilling]
B --> C[Likelihood filter]
C --> D[Pairing and developability]
D --> E[Optional assays]Стадии pipeline
| Стадия | Архитектурный класс | Что происходит | Генерация или оценка | Generator | Промежуточный объект | Альтернативы |
|---|---|---|---|---|---|---|
| Infilling generation | Autoregressive infilling LM | Заполняется masked span | generation | iglm | VH or VL sequences | PALM-H3 |
| Likelihood filter | Model likelihood | Naturalness ranking | evaluation | NR | Filtered sequences | NR |
| Pairing / structure / developability | External | VH/VL pairing и прочие checks | external_evaluation | NR | Paired candidates | AbNatiV / BioPhi / OASis |
| Assays | NR | Binding if claimed | experiment | NR | Assayed sequences | NR |
Hardware и runtime
Usually modest. Academic license; commercial license required.
Evidence level
Retrospective naturalness/diversity. No antigen conditioning.
Точки отказа
- Independent chain generation without pairing.
- Likelihood as specificity.
Критерии решения
- Нужен antigen? Нет, не этот workflow.
- Commercial use license?