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Joint CDR sequence–structure design

Co-design CDR sequence и геометрии.

Generative task

Биологическая и инженерная цель

Согласовать identity residues CDR с loop geometry и, часто, antigen interface.

Стратегия	Что генерирует	Представление	Примеры	Ограничение	Sampling	Novel topology	Integrated scoring	Complexity
Diffusion co-design	Sequence и CDR geometry	Equivariant 3D representation	DiffAb	Высокая стоимость sampling; у DiffAb нет prospective wet-lab	Joint denoising of type/position/orientation	В пределах CDR	Energy/structural metrics	Denoising steps × residues
Full-atom geometric generation	Sequence и атомные координаты	Atom/residue graph	dyMEAN, AbDiffuser	Сложная подготовка complex input	Iterative equivariant updates or diffusion	Ограничена antibody format	DockQ/ddG or physics priors	Atoms × iterations
Flow matching	Sequence–structure pair	Continuous geometric state	FlowDesign	Ограниченная независимая validation; public code NR	Flow-matching trajectory	В пределах CDR	Structure/energy metrics	Integration steps

Архитектурное решение	Практическое следствие
Requires complex structural context	Плохой input complex ломает generation.
Energy metrics in evaluation	Не равны measured affinity.

Инструмент	Generated object	Публикация	Evidence
AbDiffuser	Full-atom antibody sequence + structure	Preprint	3 prospective binding + expression validation
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
FlowDesign	CDR sequence and structure	Peer-reviewed	3–4 prospective binding/neutralization validation
RFantibody	CDR backbones, CDR sequences, antibody–target complex proposals	Peer-reviewed	3–4 prospective binding and functional validation

DiffAb/dyMEAN — in silico; FlowDesign/AbDiffuser — узкий prospective context, с оговорками.