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Antigen-conditioned CDR co-design

Практический сценарий

Есть antibody–antigen complex context; нужно co-design CDR sequence и geometry.

Вход

antigen–antibody complex
framework
CDR masks

Pipeline diagram

Joint sequence–structure sampling

→

Energy/structure metrics

→

Independent complex prediction

→

Experimental tests

Mermaid diagram

flowchart TD
    A[Antibody-antigen complex + CDR mask] --> B[Joint generator]
    B --> C[CDR sequence-structure]
    C --> D[Energy / DockQ / ddG]
    D --> E[Independent complex predictor]
    E --> F[Optional assays]

Стадии pipeline

Стадия	Архитектурный класс	Что происходит	Генерация или оценка	Generator	Промежуточный объект	Альтернативы
Joint sequence–structure sampling	Equivariant diffusion / GNN / flow matching	Обновляются residue type и geometry	generation	diffab	CDR proposals	dyMEAN, FlowDesign, AbDiffuser
Energy/structure metrics	Computational scorers	Ранжирование по energy/DockQ/ddG	evaluation	NR	Ranked designs	DockQ / TM-score
Independent complex prediction	External predictor	Проверка вне generator	external_evaluation	NR	Filtered set	AlphaFold3
Experimental tests	NR	Если переходите в wet-lab	experiment	NR	Assayed clones	NR

Hardware и runtime

GPU required. DiffAb repository archived. FlowDesign public code NR.

Evidence level

DiffAb/dyMEAN: 1–2 in silico. FlowDesign/AbDiffuser: narrow prospective, with caveats.

Точки отказа

No input complex.
Energy as affinity.
Archived code.

Критерии решения

Нужен prospective open pipeline? Лучше RFantibody.
Нужен методологический co-design benchmark? DiffAb.

Связанные задачи

Joint CDR sequence–structure design, Antigen-conditioned antibody design

Связанные инструменты

DiffAb, dyMEAN, FlowDesign, AbDiffuser

Архитектуры

Joint sequence–structure diffusion, Flow matching, SE(3)-equivariant networks

Papers

Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures, End-to-End Full-Atom Antibody Design, Flow matching for antibody CDR sequence–structure co-design

Source-grounded notes

verified Последняя сверка источников: 2026-08-20. Текст перенесён из content/research (block YAML). Provenance-метки в абзацах сохранены, если они были в исходнике.

Нужен комплекс

[PAPER]DiffAb не заменяет epitope targeting без структуры комплекса. HDOCK — внешний docking, не генератор CDR. [PAPER]