Antigen-conditioned antibody design
Дизайн antibody, conditioned на antigen/epitope.
Generative taskБиологическая и инженерная цель
Сгенерировать paratope под конкретный antigen surface или epitope sequence.
Возможные исходные данные
- antigen structure or sequence
- epitope/hotspots
- framework
Что именно генерируется
- CDR sequence/structure and optional complex
Классы генераторов
- target-conditioned-binder
- sequence-generator
Какие архитектурные подходы используются
| Стратегия | Что генерирует | Представление | Примеры | Ограничение | Sampling | Novel topology | Integrated scoring | Complexity |
|---|---|---|---|---|---|---|---|---|
| Structure-conditioned diffusion | CDR sequence–structure | 3D complex | DiffAb, RFantibody | Нужен quality complex/target structure | Conditional generation | CDRs | Complex metrics | Complex size × steps |
| Antigen sequence encoder + CDR decoder | CDR-H3 sequence | Tokens | PALM-H3 | Нет native 3D generator | Autoregressive | Нет | Learned affinity predictor | Antigen length + CDR length |
Architecture-to-workflow consequences
| Архитектурное решение | Практическое следствие |
|---|---|
| Learned affinity ranker | Не является experimental affinity. |
Compute и deployment
- Sequence-conditioned дешевле structure-conditioned.
Доступные инструменты
| Инструмент | Generated object | Публикация | Evidence |
|---|---|---|---|
| DiffAb | CDR sequence + backbone/geometry; interface proposal | NeurIPS 2022 main track (A*) | 1–2 in silico / retrospective |
| dyMEAN | Full-atom antibody sequence/structure and docked complex | ICML 2023 main track (A*) | 1–2 in silico / retrospective |
| PALM-H3 | CDR-H3 sequence; grafted antibody candidates | Peer-reviewed | 3–4 prospective binding and functional validation |
| RFantibody | CDR backbones, CDR sequences, antibody–target complex proposals | Peer-reviewed | 3–4 prospective binding and functional validation |
| tFold System | CDR sequences, candidate antibody structures and antibody–antigen complexes | Peer-reviewed | 3–5 prospective binding, epitope and developability evidence |
Типовые workflows
- Target-conditioned de novo antibody (RFantibody)
- Antigen-conditioned CDR-H3 generation (PALM-H3)
- Epitope-specific mAb CDR generation (tFold)
- Antigen-conditioned CDR co-design
Evidence summary
Структурный epitope: RFantibody/tFold. Sequence epitope: PALM-H3, узкий antigen family.
Что нельзя сравнивать напрямую
- Antigen sequence conditioning ≠ antigen structure conditioning.
Как выбирать
- Есть target structure — RFantibody.
- Есть только antigen sequence — PALM-H3, с осторожностью.