Learning to design protein-protein interactions with enhanced generalization
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arXiv
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| Autori principali: | , , , , , , , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2023
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| Soggetti: | |
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| _version_ | 1866911800023318528 |
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| author | Bushuiev, Anton Bushuiev, Roman Kouba, Petr Filkin, Anatolii Gabrielova, Marketa Gabriel, Michal Sedlar, Jiri Pluskal, Tomas Damborsky, Jiri Mazurenko, Stanislav Sivic, Josef |
| author_facet | Bushuiev, Anton Bushuiev, Roman Kouba, Petr Filkin, Anatolii Gabrielova, Marketa Gabriel, Michal Sedlar, Jiri Pluskal, Tomas Damborsky, Jiri Mazurenko, Stanislav Sivic, Josef |
| contents | Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2310_18515 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Learning to design protein-protein interactions with enhanced generalization Bushuiev, Anton Bushuiev, Roman Kouba, Petr Filkin, Anatolii Gabrielova, Marketa Gabriel, Michal Sedlar, Jiri Pluskal, Tomas Damborsky, Jiri Mazurenko, Stanislav Sivic, Josef Machine Learning Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase. |
| title | Learning to design protein-protein interactions with enhanced generalization |
| topic | Machine Learning |
| url | https://arxiv.org/abs/2310.18515 |