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| Main Authors: | , , |
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| Format: | Preprint |
| Published: |
2025
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2508.11641 |
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| _version_ | 1866911106770927616 |
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| author | Scott, Cory B. Rothschild, Charlie Nye, Benjamin |
| author_facet | Scott, Cory B. Rothschild, Charlie Nye, Benjamin |
| contents | We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to render images of proteins, it has not, to our knowledge, been widely adopted in a machine learning setting. Mirroring recent successful work applying SDFs to represent 3D geometry, we present a proof of concept that this representation of proteins could be useful in several biologically relevant applications. We also propose further experiments that are necessary to validate the proposed approach. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2508_11641 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Implicitly and Differentiably Representing Protein Surfaces and Interfaces Scott, Cory B. Rothschild, Charlie Nye, Benjamin Biomolecules We introduce a pipeline for representing a protein, or protein complex, as the union of signed distance functions (SDFs) by representing each atom as a sphere with the appropriate radius. While this idea has been used previously as a way to render images of proteins, it has not, to our knowledge, been widely adopted in a machine learning setting. Mirroring recent successful work applying SDFs to represent 3D geometry, we present a proof of concept that this representation of proteins could be useful in several biologically relevant applications. We also propose further experiments that are necessary to validate the proposed approach. |
| title | Implicitly and Differentiably Representing Protein Surfaces and Interfaces |
| topic | Biomolecules |
| url | https://arxiv.org/abs/2508.11641 |