Reciprocal best structure hits: using AlphaFold models to discover distant homologues
Open accessPublished version of a preprint
Abstract
Motivation: The conventional methods to detect homologous protein pairs use the comparison of protein sequences. But the sequences of two homologous proteins may diverge significantly and consequently may be undetectable by standard approaches. The release of the AlphaFold 2.0 software enables the prediction of highly accurate protein structures and opens many opportunities to advance our understanding of protein functions, including the detection of homologous protein structure pairs. Results: In this proof-of-concept work, we search for the closest homologous protein pairs using the structure models of five model organisms from the AlphaFold database. We compare the results with homologous protein pairs detected by their sequence similarity and show that the structural matching approach finds a similar set of results. In addition, we detect potential novel homologs solely with the structural matching approach, which can help to understand the function of uncharacterized proteins and make previously overlooked connections between well-characterized proteins. We also observe limitations of our implementation of the structure-based approach, particularly when handling highly disordered proteins or short protein structures. Our work shows that high accuracy protein structure models can be used to discover homologous protein pairs, and we expose areas for improvement of this structural matching approach. Availability and Implementation: Information to the discovered homologous protein pairs can be found at the following URL: https://doi.org/10.17863/CAM.87873. The code can be accessed here: https://github.com/VivianMonzon/Reciprocal_Best_Structure_Hits. Supplementary information: Supplementary data are available at Bioinformatics Advances online.
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,260 · 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
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. E., & Barton, G. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp033 · Cited by 10,011 · see citing works
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850 · see citing works
Pfam: The protein families database in 2021
Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa913 · Cited by 7,452 · see citing works
Self-citationUniProt: the universal protein knowledgebase in 2021
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372 · see citing works
Self-citationA genomic perspective on protein families.
Tatusov, R., Koonin, E., & Lipman, D. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,777 · see citing works
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · see citing works
Self-citationFast 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
The relation between the divergence of sequence and structure in proteins.
Chothia, C., & Lesk, A. M. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04288.x · Cited by 2,458 · see citing works
Mi, H., Ebert, D., Muruganujan, A., Mills, C., Albou, L., Mushayamaha, T., & Thomas, P. D. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1106 · Cited by 1,316 · see citing works
An integrative approach to ortholog prediction for disease-focused and other functional studies
Hu, Y., Flockhart, I., Vinayagam, A., Bergwitz, C., Berger, B., Perrimon, N., & Mohr, S. E. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-357 · Cited by 801 · see citing works
AlphaFold and Implications for Intrinsically Disordered Proteins
Ruff, K. M., & Pappu, R. V. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167208 · Cited by 635 · see citing works
Recruitment of RNA polymerase III to its target promotersPreprint
Schramm, L., & Hernandez, N. (2002) · Genes & Development · doi:10.1101/gad.1018902 · Cited by 629 · see citing works
The quest for orthologs: finding the corresponding gene across genomes
Kuzniar, A., van Ham, R. C. H. J., Pongor, S., & Leunissen, J. A. M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.08.009 · Cited by 295 · see citing works
Where does fission yeast sit on the tree of life?
Sipiczki, M. (2000) · Genome biology · doi:10.1186/gb-2000-1-2-reviews1011 · Cited by 243 · see citing works
20S Proteasome Assembly Is Orchestrated by Two Distinct Pairs of Chaperones in Yeast and in Mammals
Tallec, B. L., Barrault, M., Courbeyrette, R., Guérois, R., Marsolier‐Kergoat, M., & Peyroche, A. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.025 · Cited by 198 · see citing works
Lee, N. N., Chalamcharla, V. R., Reyes‐Turcu, F. E., Mehta, S. S., Zofall, M., Balachandran, V., Dhakshnamoorthy, J., Taneja, N., Yamanaka, S., Zhou, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.027 · Cited by 185 · see citing works
Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?
Natalie, W., & Moreno‐Hagelsieb, G. (2014) · PLoS ONE · doi:10.1371/journal.pone.0101850 · Cited by 177 · see citing works
The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A
Srinivasan, M., Mehta, P., Yu, Y., Prugar, E., Koonin, E. V., Karzai, A. W., & Sternglanz, R. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.343 · Cited by 174 · see citing works
A genome-wide resource of cell cycle and cell shape genes of fission yeast
Hayles, J., Wood, V., Jeffery, L., Hoe, K., Kim, D.-U., Park, H.-O., Salas-Pino, S., Heichinger, C., & Nurse, P. (2013) · Open Biology · doi:10.1098/rsob.130053 · Cited by 171 · see citing works
Self-citationYeast homolog of a cancer‐testis antigen defines a new transcription complex
Kisseleva-Romanova, E., Lopreiato, R., Baudin-Baillieu, A., Rousselle, J., Ilan, L., Hofmann, K., Namane, A., Mann, C., & Libri, D. (2006) · EMBO Journal · doi:10.1038/sj.emboj.7601235 · Cited by 156 · see citing works
Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?
Wood, V., Lock, A., Harris, M. A., Rutherford, K., Bähler, J., & Oliver, S. G. (2019) · Open Biology · doi:10.1098/rsob.180241 · Cited by 132 · see citing works
Self-citationA Large-Scale Screen in S. pombe Identifies Seven Novel Genes Required for Critical Meiotic Events
Martı́n-Castellanos, C., Blanco, M., Rozalén, A. E., Pérez-Hidalgo, L., García, A. I. M., Conde, F., Mata, J., Ellermeier, C., Davis, L., San-Segundo, P. A., et al. (2005) · Current Biology · doi:10.1016/j.cub.2005.10.038 · Cited by 115 · see citing works
Fission stories: using PomBase to understand Schizosaccharomyces pombe biology
Harris, M. A., Rutherford, K., Hayles, J., Lock, A., Bähler, J., Oliver, S. G., Mata, J., & Wood, V. (2021) · Genetics · doi:10.1093/genetics/iyab222 · Cited by 99 · see citing works
Self-citationPalancade, B., Zuccolo, M., Loeillet, S., Nicolas, A. G., & Doye, V. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e05-06-0527 · Cited by 95 · see citing works
Fission stories: using PomBase to understand Schizosaccharomyces pombe biology
Harris, M. A., Rutherford, K., Hayles, J., Lock, A., Bähler, J., Oliver, S. G., Mata, J., & Wood, V. (2021) · UCL Discovery (University College London) · doi:10.17863/cam.78142 · Cited by 83 · see citing works
Self-citationThe ubiquitous and ancient ER membrane protein complex (EMC): tether or not?
Wideman, J. G. (2015) · F1000Research · doi:10.12688/f1000research.6944.1 · Cited by 78 · see citing works
Machyna, M., Neugebauer, K. M., & Staněk, D. (2015) · RNA Biology · doi:10.1080/15476286.2015.1034923 · Cited by 76 · see citing works
The ubiquitous and ancient ER membrane protein complex (EMC): tether or not?
Wideman, J. G. (2015) · F1000Research · doi:10.12688/f1000research.6944.2 · Cited by 74 · see citing works
New Tools in Orthology Analysis: A Brief Review of Promising Perspectives
Nichio, B. T. D. L., Marchaukoski, J. N., & Raittz, R. T. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00165 · Cited by 71 · see citing works
Wan, L. C. K., Maisonneuve, P., Szilard, R. K., Lambert, J., Ng, T. F., Manczyk, N., Huang, H., Laister, R. C., Caudy, A. A., Gingras, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1181 · Cited by 64 · see citing works
Fission stories: Using PomBase to understand Schizosaccharomyces pombe biologyPreprint
Harris, M. A., Rutherford, K., Hayles, J., Lock, A., Bähler, J., Oliver, S. G., Mata, J., & Wood, V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.07.459264 · Cited by 57 · see citing works
Self-citationZhang, W., Collinet, B., Graille, M., Daugeron, M., Lazar, N., Libri, D., Christiane, D. D., & TILBEURGH, H. V. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv155 · Cited by 49 · see citing works
PomBase: The Scientific Resource for Fission Yeast
Lock, A., Rutherford, K., Harris, M. A., & Wood, V. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7737-6_4 · Cited by 40 · see citing works
Self-citationCross-phyla protein annotation by structural prediction and alignment
Ruperti, F., Papadopoulos, N., Musser, J. M., Mirdita, M., Steinegger, M., & Arendt, D. (2023) · Genome Biology · doi:10.1186/s13059-023-02942-9 · Cited by 38 · see citing works
Schizosaccharomyces pombe rsm1 genetically interacts with spmex67, which is involved in mRNA export.
Yoon, J. H. (2004) · PubMed · Cited by 10 · see citing works
Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression
Walton, S. J., Wang, H., Quintero-Cadena, P., Bateman, A. G., & Sternberg, P. W. (2020) · Genetics · doi:10.1534/genetics.120.302923 · Cited by 6 · see citing works
Self-citationReciprocal Best Structure Hits (RBSH)
Monzon, V., Paysan‐Lafosse, T., Wood, V., & Bateman, A. (2022) · Apollo (University of Cambridge) · doi:10.17863/cam.87873 · Cited by 1 · see citing works
Self-citation
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Cited by
Sorted by citations
The Pfam protein families database: embracing AI/ML
Paysan-Lafosse, T., Andreeva, A., Blum, M., Chuguransky, S., Grego, T., Pinto, B. L., Salazar, G. A., Bileschi, M. L., Llinares-López, F., Meng-Papaxanthos, L., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae997 · Cited by 382 · see citing works
Self-citationPomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability
Rutherford, K., Lera-Ramírez, M., & Wood, V. (2024) · Genetics · doi:10.1093/genetics/iyae007 · Cited by 101 · see citing works
Self-citationThe origin and structural evolution of de novo genes in Drosophila
Peng, J., & Zhao, L. (2024) · Nature Communications · doi:10.1038/s41467-024-45028-1 · Cited by 72 · see citing works
Barrera‐Redondo, J., Lotharukpong, J. S., Drost, H., & Coelho, S. M. (2023) · Genome biology · doi:10.1186/s13059-023-02895-z · Cited by 61 · see citing works
Cross-phyla protein annotation by structural prediction and alignment
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Malbranke, C., Bikard, D., Cocco, S., Monasson, R., & Tubiana, J. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102571 · Cited by 37 · see citing works
Is Protein BLAST a thing of the past?
Al-Fatlawi, A. H., Menzel, M., & Schroeder, M. (2023) · Nature Communications · doi:10.1038/s41467-023-44082-5 · Cited by 32 · see citing works
Marrero, M. C., Capdevielle, S., Huang, W., Al‐Subhi, A. M., Busscher, M., Busscher‐Lange, J., van der Wal, F., de Ridder, D., van Dijk, A. D. J., Hogenhout, S. A., et al. (2023) · The Plant Journal · doi:10.1111/tpj.16546 · Cited by 31 · see citing works
Xie, X., Deng, X., Chen, L., Yuan, J., Chen, H., Wei, C., Liu, X., Wuertz, S., & Qiu, G. (2023) · Environmental Science and Ecotechnology · doi:10.1016/j.ese.2023.100353 · Cited by 31 · see citing works
Vijayakumar, S., Swetha, R. G., Bakthavatchalam, Y. D., Vasudevan, K., Shankar, B. A., Kirubananthan, A., Walia, K., Ramaiah, S., Biswas, I., Veeraraghavan, B., et al. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.02511-23 · Cited by 27 · see citing works
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Andorf, C. M., Sen, S., Hayford, R. K., Portwood, J. L., Cannon, E. K. S., Harper, L. C., Gardiner, J. M., Sen, T. Z., & Woodhouse, M. R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.10.516002 · Cited by 9 · see citing works
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Maize protein structure resources at the maize genetics and genomics database
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Muthye, V., & Wasmuth, J. D. (2023) · Frontiers in Parasitology · doi:10.3389/fpara.2023.1162697 · Cited by 8 · see citing works
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Deng, X., Yao, Q., Horváth, A., Jiang, Z., Zhao, J., Fischer, T., & Sugiyama, T. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae463 · Cited by 7 · see citing works
OAF: a new member of the BRICHOS family
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Expanding kinetoplastid genome annotation through protein structure comparison
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Hashimoto, H., Ramirez, D. H., Lautier, O., Pawlak, N., Blobel, G., Palancade, B., & Debler, E. W. (2022) · Scientific Reports · doi:10.1038/s41598-022-22183-3 · Cited by 4 · see citing works
AlphaFold2 predicts interactions amidst confounding structural compatibilityPreprint
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Lyapina, I., Ganaeva, D., Rogozhin, E. A., Ryabukhina, E. V., Ryazantsev, D. Y., Lazarev, V., Alieva, S. E., Mamaeva, A., & Fesenko, I. (2025) · Physiologia Plantarum · doi:10.1111/ppl.70147 · Cited by 3 · see citing works
Xie, X., Deng, X., Chen, L., Yuan, J., Chen, H., Wei, C., Liu, X., Wuertz, S., & Qiu, G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.20.558572 · Cited by 2 · see citing works
Rad, A. A., Fayazi, J., Nassiri, M. T. B., & Baferani, A. R. H. (2022) · Research in Molecular Medicine · doi:10.32598/rmm.10.4.1076.4 · Cited by 1 · see citing works
Hendrawati, A., Ayuningrum, D., Sabdaningsih, A., & Amalia, R. (2024) · Asia-Pacific Journal of Molecular Biology and Biotechnology · doi:10.35118/apjmbb.2024.032.2.14 · Cited by 1 · see citing works
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Sharma, S., Ponniah, K., Bandyopadhyay, I., Vadawale, D., Koushika, S. P., & Ghosh‐Roy, A. (2026) · PLoS Genetics · doi:10.1371/journal.pgen.1012106 · Cited by 1 · see citing works
Kalepu, R., Hassan, M., Hamid, A. A. A., Mohd‐Assaad, N., & Muhammad, N. A. N. (2026) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-026-00904-4 · Cited by 1 · see citing works
Vosseberg, J. (2022) · doi:10.33540/22
Muthye, V., & Wasmuth, J. D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.08.527763
Sharma, S., Ponniah, K., & Ghosh‐Roy, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.24.650367
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Barrera‐Redondo, J., Lotharukpong, J. S., Drost, H.-G., & Coelho, S. M. (2023) · Figshare · doi:10.6084/m9.figshare.22620406
Barrera‐Redondo, J., Lotharukpong, J. S., Drost, H.-G., & Coelho, S. M. (2023) · Figshare · doi:10.6084/m9.figshare.22620391
Comparative performance of structural aligners in functional domain annotation
Borujeni, P. M., & Salavati, R. (2026) · Journal of Structural Biology · doi:10.1016/j.jsb.2026.108308
Deep homology and design of proteasome chaperone proteins in Candidozyma auris
Rapala, J. R., Siddiq, M. A., Wittkopp, P. J., O’Meara, M. J., & O’Meara, T. R. (2026) · Nature Communications · doi:10.1038/s41467-026-71206-4
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san, S. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7519214
- Authors
- Monzon, V., Paysan-Lafosse, T., Wood, V., & Bateman, A.
- Affiliations
- European Bioinformatics Institute (GB)
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton CB21 4HH, UK
- University of Cambridge (GB)
- Corresponding author
- Monzon, Vivian
- Venue
- Bioinformatics Advances
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-01-01
- Volume
- 2
- Issue
- 1
- Pages
- vbac072-vbac072
- ISSN
- 2635-0041 (ISSN-L)
- PMC
- PMC9666668
- OpenAlex
- W4303184143
- Cited by
- 46
- References
- 41
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 13 · 2023: 16 · 2022: 6
- FWCI
- 3.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Bioinformatics Advances (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, public-domain)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Wellcome Trust (218236/Z/19/Z)
- 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 › Genomics and Phylogenetic Studies
- Keywords
- AlphaFold, protein structure prediction, sequence divergence, protein function prediction, protein disorder, model organisms
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