Fast protein structure searching using structure graph embeddings
Open accessPublished version of a preprint
Abstract
Comparing and searching protein structures independent of primary sequence has proved useful for remote homology detection, function annotation, and protein classification. Fast and accurate methods to search with structures will be essential to make use of the vast databases that have recently become available, in the same way that fast protein sequence searching underpins much of bioinformatics. We train a simple graph neural network using supervised contrastive learning to learn a low-dimensional embedding of protein domains. Availability and implementation: The method, called Progres, is available as software at https://github.com/greener-group/progres and as a web server at https://progres.mrc-lmb.cam.ac.uk. It has accuracy comparable to the best current methods and can search the AlphaFold database TED domains in a 10th of a second per query on CPU.
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Cites
Adam: A Method for Stochastic Optimization
Kingma, D. P., & Ba, J. (2014) · arXiv · doi:10.48550/arxiv.1412.6980 · Cited by 98,946 · see citing works
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Evolutionary-scale prediction of atomic level protein structure with a language model
Lin, Z., Akin, H., Rao, R., Hie, B., Zhu, Z., Lu, W., Smetanin, N., Verkuil, R., Kabeli, O., Shmueli, Y., et al. (2022) · doi:10.1101/2022.07.20.500902 · Cited by 5,523 · see citing works
Fast and accurate protein structure search with Foldseek
van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2022) · doi:10.1101/2022.02.07.479398 · Cited by 2,598 · see citing works
Fast and accurate protein structure search with Foldseek
van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01773-0 · Cited by 2,596 · see citing works
ECOD: an evolutionary classification of protein domains
Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B.-H., & Grishin, N. V. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003926 · Cited by 426 · cited 5× · see citing works
“A t-SNE embedding for the AlphaFold database TED domains compared to ECOD ( Cheng et al. 2014) and the AlphaFold 21 organisms set (Varadi et al. 2022, Bordin et al. 2023) shows the volume of new structural information available in the AlphaFold database.”
InfluentialAlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms
Bordin, N., Sillitoe, I., Nallapareddy, V., Rauer, C., Lam, S. D., Waman, V. P., Sen, N., Heinzinger, M., Littmann, M., Kim, S., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-04488-9 · Cited by 103 · see citing works
Chainsaw: protein domain segmentation with fully convolutional neural networks
Wells, J., Hawkins-Hooker, A., Bordin, N., Sillitoe, I., Paige, B., & Orengo, C. (2023) · doi:10.1101/2023.07.19.549732 · Cited by 53 · see citing works
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- Authors
- Greener, J. G., & Jamali, K.
- Affiliations
- MRC Laboratory of Molecular Biology (GB)
- Corresponding author
- Greener, Joe G
- Venue
- Bioinformatics Advances
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-03-05
- Volume
- 5
- Issue
- 1
- Pages
- vbaf042-vbaf042
- ISSN
- 2635-0041 (ISSN-L)
- PMC
- PMC11974391
- OpenAlex
- W4409217924
- Cited by
- 19
- References
- 8
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 4 · 2023: 2
- FWCI
- 2.31
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Bioinformatics Advances (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Funders
- Medical Research Council
- United Kingdom Research and Innovation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- protein structure search, graph neural networks, supervised contrastive learning, protein domains, remote homology detection, protein classification, AlphaFold, PROGRES
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