A method for multiple-sequence-alignment-free protein structure prediction using a protein language model
Open accessPublished version of a preprint
Abstract
Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on multiple sequence alignments (MSAs) as inputs to learn the co-evolution information from the homologous sequences. Nonetheless, searching MSAs from protein databases is time consuming, usually taking tens of minutes. Consequently, we attempt to explore the limits of fast protein structure prediction by using only primary structures of proteins. Our proposed method, HelixFold-Single, combines a large-scale protein language model with the superior geometric learning capability of AlphaFold2. HelixFold-Single first pre-trains a large-scale protein language model with thousands of millions of primary structures utilizing the self-supervised learning paradigm, which will be used as an alternative to MSAs for learning the co-evolution information. Then, by combining the pre-trained protein language model and the essential components of AlphaFold2, we obtain an end-to-end differentiable model to predict the three-dimensional coordinates of atoms from only the primary structure. HelixFold-Single is validated on datasets CASP14 and CAMEO, achieving competitive accuracy with the MSA-based methods on targets with large homologous families. Furthermore, HelixFold-Single consumes much less time than the mainstream pipelines for protein structure prediction, demonstrating its potential in tasks requiring many predictions.
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Cites
Highly accurate protein structure prediction with AlphaFold
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Self-citation
- Authors
- Fang, X., Wang, F., Liu, L., He, J., Lin, D., Xiang, Y., Zhu, K., Zhang, X., Wu, H., Li, H., & Song, L.
- Affiliations
- Baidu (China) (CN)
- Corresponding author
- Wang, Fan
- Song, Le
- ORCID
- Venue
- Nature Machine Intelligence
- Published
- 2023-10-09
- Volume
- 5
- Issue
- 10
- Pages
- 1087-1096
- ISSN
- 2522-5839 (ISSN-L)
- OpenAlex
- W4387451333
- Cited by
- 132
- References
- 11
- Citations by year
- 2026: 30 · 2025: 30 · 2024: 48 · 2023: 21 · 2022: 3
- FWCI
- 11.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Machine Intelligence (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein structure prediction, protein language models, primary structure, AlphaFold2, self-supervised learning, CASP14, cameos, homologous sequences
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