Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2
Fuente:
arXiv
Salvato in:
| Autori principali: | , , , |
|---|---|
| Natura: | Preprint |
| Pubblicazione: |
2024
|
| Soggetti: | |
| Accesso online: | |
| Tags: |
Aggiungi Tag
Nessun Tag, puoi essere il primo ad aggiungerne!!
|
| _version_ | 1866929357501497344 |
|---|---|
| author | Lin, Yeqing Lee, Minji Zhang, Zhao AlQuraishi, Mohammed |
| author_facet | Lin, Yeqing Lee, Minji Zhang, Zhao AlQuraishi, Mohammed |
| contents | Protein diffusion models have emerged as a promising approach for protein design. One such pioneering model is Genie, a method that asymmetrically represents protein structures during the forward and backward processes, using simple Gaussian noising for the former and expressive SE(3)-equivariant attention for the latter. In this work we introduce Genie 2, extending Genie to capture a larger and more diverse protein structure space through architectural innovations and massive data augmentation. Genie 2 adds motif scaffolding capabilities via a novel multi-motif framework that designs co-occurring motifs with unspecified inter-motif positions and orientations. This makes possible complex protein designs that engage multiple interaction partners and perform multiple functions. On both unconditional and conditional generation, Genie 2 achieves state-of-the-art performance, outperforming all known methods on key design metrics including designability, diversity, and novelty. Genie 2 also solves more motif scaffolding problems than other methods and does so with more unique and varied solutions. Taken together, these advances set a new standard for structure-based protein design. Genie 2 inference and training code, as well as model weights, are freely available at: https://github.com/aqlaboratory/genie2. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2405_15489 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2 Lin, Yeqing Lee, Minji Zhang, Zhao AlQuraishi, Mohammed Biomolecules Machine Learning Protein diffusion models have emerged as a promising approach for protein design. One such pioneering model is Genie, a method that asymmetrically represents protein structures during the forward and backward processes, using simple Gaussian noising for the former and expressive SE(3)-equivariant attention for the latter. In this work we introduce Genie 2, extending Genie to capture a larger and more diverse protein structure space through architectural innovations and massive data augmentation. Genie 2 adds motif scaffolding capabilities via a novel multi-motif framework that designs co-occurring motifs with unspecified inter-motif positions and orientations. This makes possible complex protein designs that engage multiple interaction partners and perform multiple functions. On both unconditional and conditional generation, Genie 2 achieves state-of-the-art performance, outperforming all known methods on key design metrics including designability, diversity, and novelty. Genie 2 also solves more motif scaffolding problems than other methods and does so with more unique and varied solutions. Taken together, these advances set a new standard for structure-based protein design. Genie 2 inference and training code, as well as model weights, are freely available at: https://github.com/aqlaboratory/genie2. |
| title | Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2 |
| topic | Biomolecules Machine Learning |
| url | https://arxiv.org/abs/2405.15489 |