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Protein language model embeddings for fast, accurate, alignment-free protein structure prediction
Open accessPreprint — published as 10.1016/j.str.2022.05.001
Abstract
All state-of-the-art (SOTA) protein structure predictions rely on evolutionary information captured in multiple sequence alignments (MSAs), primarily on evolutionary couplings (co-evolution). Such information is not available for all proteins and is computationally expensive to generate. Prediction models based on Artificial Intelligence (AI) using only single sequences as input are easier and cheaper but perform so poorly that speed becomes irrelevant. Here, we described the first competitive AI solution exclusively inputting embeddings extracted from pre-trained protein Language Models (pLMs), namely from the transformer pLM ProtT5, from single sequences into a relatively shallow (few free parameters) convolutional neural network (CNN) trained on inter-residue distances, i.e. protein structure in 2D. The major advance originated from processing the attention heads learned by ProtT5. Although these models required at no point any MSA, they matched the performance of methods relying on co-evolution. Although not reaching the very top, our lean approach came close at substantially lower costs thereby speeding up development and each future prediction. By generating protein-specific rather than family-averaged predictions, these new solutions could distinguish between structural features differentiating members of the same family of proteins with similar structure predicted alike by all other top methods.
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Human O-linked Glycosylation Site Prediction Using Pretrained Protein Language ModelPreprint
Pakhrin, S. C., Chauhan, N., Khan, S., Upadhyaya, J., Keller, C., Neuman, L. N., Beck, M. R., & Blanco, E. (2023) · Research Square · doi:10.21203/rs.3.rs-3587524/v1 · Cited by 3
Liu, Y., Wang, X., Zhong, H., Zhai, J., Gong, X., & Lu, T. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf242 · Cited by 2
Chen, G., Liao, J., Yu, Y., Le, K., Zhao, H., Qin, Y., Cai, L., & Sheng, R. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01753 · Cited by 4
Dock2D: Synthetic Data for the Molecular Recognition Problem
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Metadata
- Authors
- Weissenow, K., Heinzinger, M., & Rost, B.
- Affiliations
- Technical University of Munich (DE)
- Corresponding author
- Weissenow, Konstantin
- Venue
- Structure
- Publisher
- openRxiv
- Published
- 2021-08-02
- Volume
- 30
- Issue
- 8
- Pages
- 1169-1177.e4
- ISSN
- 0969-2126 (ISSN-L)
- OpenAlex
- W4281291878
- Cited by
- 139
- References
- 91
- Citations by year
- 2026: 21 · 2025: 30 · 2024: 34 · 2023: 30 · 2022: 19 · 2021: 5
- FWCI
- 9.22
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Structure (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Alexander von Humboldt-Stiftung
- Nvidia
- Deutsche Forschungsgemeinschaft (DFG-GZ: RO1320/4-1, RO1320/4\u20131, RO1320/4‐1)
- Bundesministerium für Bildung und Forschung
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein structure prediction, protein language models, ProtT5, attention heads, convolutional neural networks, protein engineering, deep mutational scanning, coevolution
- MeSH terms
- Artificial Intelligence, Language, Proteins, Sequence Alignment, Computational Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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