Fast uncovering of protein sequence diversity from structure
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arXiv
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| Autores principales: | , , , |
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| Formato: | Preprint |
| Publicado: |
2024
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| Materias: | |
| Acceso en línea: | |
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| _version_ | 1866913865550266368 |
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| author | Silva, Luca Alessandro Meynard-Piganeau, Barthelemy Lucibello, Carlo Feinauer, Christoph |
| author_facet | Silva, Luca Alessandro Meynard-Piganeau, Barthelemy Lucibello, Carlo Feinauer, Christoph |
| contents | We present InvMSAFold, an inverse folding method for generating protein sequences that is optimized for diversity and speed. For a given structure, InvMSAFold generates the parameters of a probability distribution over the space of sequences with pairwise interactions, capturing the amino acid covariances observed in Multiple Sequence Alignments (MSA) of homologous proteins. This allows for the efficient generation of highly diverse protein sequences while preserving structural and functional integrity. We show that this increased diversity in sampled sequences translates into greater variability in biochemical properties, highlighting the exciting potential of our method for applications such as protein design. The orders of magnitude improvement in sampling speed compared to existing methods unlocks new possibilities for high-throughput virtual screening. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2406_11975 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Fast uncovering of protein sequence diversity from structure Silva, Luca Alessandro Meynard-Piganeau, Barthelemy Lucibello, Carlo Feinauer, Christoph Quantitative Methods We present InvMSAFold, an inverse folding method for generating protein sequences that is optimized for diversity and speed. For a given structure, InvMSAFold generates the parameters of a probability distribution over the space of sequences with pairwise interactions, capturing the amino acid covariances observed in Multiple Sequence Alignments (MSA) of homologous proteins. This allows for the efficient generation of highly diverse protein sequences while preserving structural and functional integrity. We show that this increased diversity in sampled sequences translates into greater variability in biochemical properties, highlighting the exciting potential of our method for applications such as protein design. The orders of magnitude improvement in sampling speed compared to existing methods unlocks new possibilities for high-throughput virtual screening. |
| title | Fast uncovering of protein sequence diversity from structure |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2406.11975 |