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Joint sequence–structure generation

Одновременная или tightly coupled генерация sequence и structure.

Generative task

Биологическая и инженерная цель

Согласовать residue identity и геометрию в одном generative process.

Стратегия	Что генерирует	Представление	Примеры	Ограничение	Sampling	Novel topology	Integrated scoring	Complexity
Multimodal masked LM	Sequence, structure tokens, function tracks	Multimodal tokens	ESM3	Confidence ≠ function	Iterative unmasking	Возможна	Model likelihood/confidence	Число tracks × unmasking steps
Joint diffusion / flow matching	Sequence + geometry	Continuous geometric state + residue types	DiffAb, FlowDesign, ProteinGenerator	Sampling cost; independent validation всё равно нужна	Denoising or flow trajectory	Зависит от модели	Energy/confidence	Steps × residues

Архитектурное решение	Практическое следствие
Integrated structure decoder	Увеличивает стоимость workflow, но даёт in-loop geometry.

Инструмент	Generated object	Публикация	Evidence
BoltzGen	Binder sequence–structure and target complex	Preprint	3–4 prospective binding/functional validation
Chroma	Backbone/all-atom structure and sequence	Peer-reviewed	3–5 early prospective biophysical/structural validation
ESM3	Sequence, structure tokens, function annotations; can co-generate modalities	Peer-reviewed	4 prospective functional validation
ProteinGenerator	Coupled sequence–structure proposals	Peer-reviewed	3–4 prospective functional validation

Coupled generation не отменяет внешнюю validation.