ProteinGuide is applied jointly with wet-lab data generation to increase the editing activity of an adenine base editor in vivo, resulting in a base editor with higher editing efficiency than was previously achieved using seven rounds of directed evolution.
This work demonstrates how to provide task-specific information without losing the general knowledge learned during pretraining by using direct preference optimization to align a structure-conditioned protein language model to preferentially generate stable protein sequences.
Talal Widatalla, Ashir Borah, Samuel H. King et al.· Nature Methods· 3 citations
This work introduces a symmetric dual-path architecture that both leverages PLMs for pretrained sequence evolution knowledge and MPLMs for pretrained structural knowledge to iteratively guide protein sequence generation.
Han-Dong Wang, Jiaxin Qi, Baisheng Lai et al.· 0 citations
A cheap density prior is introduced over natural protein activations and keeps only the candidates that remain typical under it, a training-free post-hoc step the authors call Mahalanobis filtering that improves both the property score and the structural plausibility of the sequences it keeps at negligible cost, withou...
Shuibai Zhang, Xin-Chi Liu, Fred Zhangzhi Peng et al.· 0 citations
Understanding and generation are often treated as two separate paradigms in training deep neural networks, despite the fact that both are trained with closely related objectives such as denoising and masked prediction. While prior studies have shown that generative models often learn suboptimal representations for unde...
Raygun is introduced, a generative artificial intelligence framework that enables miniaturization, modification and augmentation of proteins, using a probabilistic encoding of protein sequences constructed from language model embeddings, enabling the kind of coordinated, large-scale sequence modifications that characte...
Kapil Devkota, Daichi Shonai, Joey Mao et al.· Nature· 1 citation
Applications to thioredoxins, visual opsins, and Tara Oceans environmental diatom cold-shock proteins show that PLMView can move from interpretable residue-level determinants in well-studied protein families to large-scale environmental functional discovery, linking molecular specialization to ecological distribution a...