Protein generation with evolutionary diffusion: sequence is all you need
Preprint| Поле | Значение |
|---|---|
| Authors | NR |
| Year | 2023/2024 |
| Venue / status | Preprint (Frontier/Watchlist) |
| DOI | 10.1101/2023.09.11.556673 |
| URL | https://doi.org/10.1101/2023.09.11.556673 |
| Preprint URL | https://doi.org/10.1101/2023.09.11.556673 |
| Tools | EvoDiff |
Задача и claimed novelty
| Поле | Значение |
|---|---|
| Main biological task | General sequence generation; sequence-space motif scaffolding; MSA-conditioned generation |
| Claimed novelty | NR |
Архитектура
| Поле | Значение |
|---|---|
| Model architecture | Discrete diffusion over amino-acid tokens; OA-DM / D3PM variants |
| Input representation | NR |
| Encoder / decoder | NR |
| Generative state | Amino-acid sequence |
| Conditioning | Sequence motif masks; MSA context; supports disordered regions |
| Sampling | NR |
Training
| Поле | Значение |
|---|---|
| Objectives / losses | NR |
| Dataset | NR |
| Preprocessing | NR |
Inference
NR
Baselines и retrospective benchmarks
| Поле | Значение |
|---|---|
| Baselines | NR |
| Retrospective | Computational sequence, structural-plausibility and motif-scaffolding evaluation |
Prospective experimental validation
| Поле | Значение |
|---|---|
| Prospective | NR |
| Tested designs | No prospective wet-lab validation in primary work |
| Success criterion | Computational sequence, structural-plausibility and motif-scaffolding evaluation |
| Main results | Computational sequence, structural-plausibility and motif-scaffolding evaluation |
Limitations
Sequence-only generator; motif presence does not establish correct 3D placement or function; prospective evidence absent.
Что статья показывает
- Computational sequence, structural-plausibility and motif-scaffolding evaluation
Чего статья не показывает
- Predicted confidence, likelihood, pLDDT, docking or developability scores are not experimental affinity.
Размеченные утверждения
| Утверждение | Тип | Локатор |
|---|---|---|
| Protein generation with evolutionary diffusion: sequence is all you need | Author-reported | DOI/URL from landscape matrix |
| Publication status: Preprint (Frontier/Watchlist) | Author-reported | landscape matrix, publication status column |
Source-grounded разбор статьи
Исследовательский вопрос
[MATRIX]General sequence generation; sequence-space motif scaffolding; MSA-conditioned generation
Утверждения и поддержка evidence
[MATRIX]Claimed novelty: NR
[INTERPRETATION]Статья не «доказывает» общее преимущество метода вне своего экспериментального дизайна.
Что представленный evidence не поддерживает
- Predicted confidence, likelihood, pLDDT, docking or developability scores are not experimental affinity.
Ограничения, признанные авторами
[MATRIX]Sequence-only generator; motif presence does not establish correct 3D placement or function; prospective evidence absent.
Дополнительные ограничения интерпретации
NRПока Methods/SI не прочитаны, нельзя утверждать split leakage, точные гиперпараметры и полноту ablation.