Fast and accurate protein structure search with Foldseek

Basic local alignment search tool

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Highly accurate protein structure prediction with AlphaFold

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AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

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Accelerated Profile HMM Searches

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Evolutionary-scale prediction of atomic level protein structure with a language model

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Accurate prediction of protein structures and interactions using a 3-track network

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Sensitive protein alignments at tree-of-life scale using DIAMOND

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MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

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TM-align: a protein structure alignment algorithm based on the TM-score

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Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.

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Training Compute-Optimal Protein Language ModelsPreprint

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Identification of a family of peptidoglycan transpeptidases reveals that Clostridioides difficile requires noncanonical cross-links for viability

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Sugar assimilation underlying dietary evolution of Neotropical bats

Camacho, J. J., Rivera, A. B., Peña, V., Morales‐Sosa, P., Robb, S. M. C., Russell, J., Yi, K., Wang, Y., Tsuchiya, D., Murillo‐García, O. E., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02485-7 · Cited by 23

Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote

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A DNA-gated molecular guard controls bacterial Hailong anti-phage defence

Tan, J. M. J., Melamed, S., Cofsky, J. C., Syangtan, D., Hobbs, S. J., del Mármol, J. I., Jost, M., Kruse, A. C., Sorek, R., & Kranzusch, P. J. (2025) · Nature · doi:10.1038/s41586-025-09058-z · Cited by 27

Protein functional site annotation using local structure embeddings

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Protein Structural Phylogenetics

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The diversity of PET degrading enzymes: A systematic review of sequence, structure, and function

Ahituv, N., Freund, D., Mireles, R., & Noda‐García, L. (2025) · Protein Science · doi:10.1002/pro.70282 · Cited by 21

The Panoptes system uses decoy cyclic nucleotides to defend against phage

Sullivan, A. E., Nabhani, A., Izrailevsky, D. S., Schinkel, K., Hoffman, C. R. K., Robbins, L. K., Nagy, T. A., Duncan, M. L., Ledvina, H. E., Erbse, A. H., et al. (2025) · Nature · doi:10.1038/s41586-025-09557-z · Cited by 27

Evaluating generalization in protein–ligand cofolding methods

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CasDinG is a 5′-3′ dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity

Domgaard, H., Cahoon, C., Armbrust, M. J., Redman, O., Jolley, A., Thomas, A., & Jackson, R. N. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad546 · Cited by 23

Structures of the Hepaci-, Pegi-, and Pestiviruses envelope proteins suggest a novel membrane fusion mechanism

Oliver, M. R., Toon, K., Lewis, C. B., Devlin, S., Gifford, R. J., & Grove, J. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002174 · Cited by 23

Assembly mechanism of a Tad secretion system secretin-pilotin complex

Tassinari, M., Rudzite, M., Filloux, A., & Low, H. H. (2023) · Nature Communications · doi:10.1038/s41467-023-41200-1 · Cited by 22

Identification of type VI secretion system effector-immunity pairs using structural bioinformatics

Geller, A. M., Shalom, M., Zlotkin, D., Blum, N., & Levy, A. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00035-8 · Cited by 22

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

Baltoumas, F. A., Karatzas, E., Páez-Espino, D., Venetsianou, N. K., Aplakidou, E., Oulas, A., Finn, R. D., Ovchinnikov, S., Pafilis, E., Kyrpides, N. C., et al. (2023) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2023.1157956 · Cited by 21

Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase

Raisinghani, N., Alshahrani, M., Gupta, G., Tian, H., Xiao, S., Tao, P., & Verkhivker, G. M. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00222 · Cited by 17

Evidence of microbial reductive dehalogenation in deep-sea cold seeps and its implications for biogeochemical cycles

Han, Y., Deng, Z., Peng, Y., Peng, J., Cao, L., Xu, Y., Yang, Y., Zhou, H., Zhang, C., Zhang, D., et al. (2025) · Microbiome · doi:10.1186/s40168-025-02147-1 · Cited by 21

The prototypic crAssphage is a linear phage-plasmid

Schmidtke, D. T., Hickey, A. S.-M., Wirbel, J., Lin, J. D., Liachko, I., Sherlock, G., & Bhatt, A. S. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.07.004 · Cited by 41

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

Kim, D. E., Watson, J. L., Juergens, D., Majumder, S., Sonigra, R., Gerben, S. R., Kang, A., Bera, A. K., Li, X., & Baker, D. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2425459122 · Cited by 21

Evolution and diversification of the ACT-like domain associated with plant basic helix–loop–helix transcription factors

Lee, Y. S., Shiu, S., & Erich Grotewold, A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2219469120 · Cited by 20

New clades of viruses infecting the obligatory biotroph Bremia lactucae representing distinct evolutionary trajectory for viruses infecting oomycetes

Forgia, M., Daghino, S., Chiapello, M., Ciuffo, M., & Turina, M. (2024) · Virus Evolution · doi:10.1093/ve/veae003 · Cited by 21

Redundant essentiality of AsmA-like proteins in Pseudomonas aeruginosa

Sposato, D., Mercolino, J., Torrini, L., Sperandeo, P., Lucidi, M., Alegiani, R., Varone, I., Molesini, G., Leoni, L., Rampioni, G., et al. (2024) · mSphere · doi:10.1128/msphere.00677-23 · Cited by 19

A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture

Attenborough, T. C. H., Rawlinson, K. A., Soria, C. L. D., Ambridge, K., Sankaranarayanan, G., Graham, J., Cotton, J. A., Doyle, S. R., Rinaldi, G., & Berriman, M. (2024) · eLife · doi:10.7554/elife.95628 · Cited by 29

Simple, Efficient, and Scalable Structure-Aware Adapter Boosts Protein Language Models

Tan, Y., Li, M., Zhou, B., Zhong, B., Zheng, L., Tan, P., Zhou, Z., Yu, H., Fan, G., & Hong, L. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c00689 · Cited by 23

ESMFold Hallucinates Native-Like Protein SequencesPreprint

Jeliazkov, J. R., del Alamo, D., & Karpiak, J. D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.23.541774 · Cited by 24

CARD-like domains mediate anti-phage defense in bacterial gasdermin systemsPreprint

Wein, T., Johnson, A. G., Millman, A., Lange, K., Yirmiya, E., Hadary, R., Garb, J., Steinruecke, F., Hill, A. B., Kranzusch, P. J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.28.542683 · Cited by 21

PneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae

Janssen, A. B., Gibson, P. S., Bravo, A. M., de Bakker, V., Slager, J., & Veening, J.-W. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae923 · Cited by 18

Unprecedented Diversity of the Glycoside Hydrolase Family 70: A Comprehensive Analysis of Sequence, Structure, and Function

Pijning, T., & Dijkhuizen, L. (2024) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.4c04807 · Cited by 21

A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses

Soh, T. K., Ognibene, S., Sanders, S., Schäper, R., Kaufer, B. B., & Bosse, J. B. (2024) · Nature Communications · doi:10.1038/s41467-024-54668-2 · Cited by 20

Integrons are anti-phage defence libraries in Vibrio parahaemolyticus

Getz, L. J., Fairburn, S. R., Liu, Y. V., Qian, A. L., & Maxwell, K. L. (2025) · Nature Microbiology · doi:10.1038/s41564-025-01927-7 · Cited by 20

Enantiocomplementary Gut Bacterial Enzymes Metabolize Dietary Polyphenols

Dong, X., Bae, M., Le, C. “., Ramos, M. A. A., & Balskus, E. P. (2025) · Journal of the American Chemical Society · doi:10.1021/jacs.4c09892 · Cited by 21

Cat1 forms filament networks to degrade NAD + during the type III CRISPR-Cas antiviral response

Baca, C. F., Majumder, P., Hickling, J. H., Patel, D. J., & Marraffini, L. A. (2025) · Science · doi:10.1126/science.adv9045 · Cited by 24

The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops

Sutherland, C. A., Stevens, D. M., Seong, K., Wei, W., & Krasileva, K. V. (2025) · The Plant Cell · doi:10.1093/plcell/koaf109 · Cited by 20

Multimeric protein interaction and complex prediction: Structure, dynamics and function

Lu, D., Yu, S., Huang, Y., & Gong, X. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.05.009 · Cited by 23

Independently evolved extracellular electron transfer pathways in ecologically diverse Desulfobacterota

Shaw, D. R., Katuri, K. P., Sapireddy, V., Douvropoulou, O., Gralnick, J. A., & Saikaly, P. E. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf097 · Cited by 21

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology

Boucher, M. J., Banerjee, S., Joshi, M. B., Wei, A. L., Nalley, M. J., Huang, M. Y., Lei, S., Ciranni, M., Condon, A., Langen, A., et al. (2024) · Cell · doi:10.1016/j.cell.2025.05.017 · Cited by 30

A de novo-originated gene drives rose scent diversification

Li, Y., Li, R., Shang, J., Zhao, K., Sui, Y., Liu, Z., Yan, H., Bao, M., Liang, M., Zhao, Q. L., et al. (2025) · Cell · doi:10.1016/j.cell.2025.08.011 · Cited by 23

Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF

Gäfe, S., & Niemann, H. H. (2023) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798323004254 · Cited by 21

Toxinome—the bacterial protein toxin database

Danov, A., Segev, O., Bograd, A., Ben-Eliyahu, Y., Dotan, N., Kaplan, T., & Levy, A. (2023) · mBio · doi:10.1128/mbio.01911-23 · Cited by 22

Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology

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Functional domain annotation by structural similarity

Borujeni, P. M., & Salavati, R. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae005 · Cited by 19

Eukaryotic genomic data uncover an extensive host range of mirusviruses

Zhao, H., Meng, L., Hikida, H., & Ogata, H. (2024) · Current Biology · doi:10.1016/j.cub.2024.04.085 · Cited by 20

The parasitic lifestyle of an archaeal symbiont

Hamm, J. N., Liao, Y., von Kügelgen, A., Dombrowski, N., Landers, E., Brownlee, C., Johansson, E. M. V., Whan, R. M., Baker, M. A. B., Baum, B., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49962-y · Cited by 16

Noncanonical inheritance of phenotypic information by protein amyloids

Eroglu, M., Zocher, T., McAuley, J., Webster, R., Xiao, M. Z. X., Yu, B., Mok, C. A., & Derry, W. B. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01494-9 · Cited by 27

Computational design of soluble functional analogues of integral membrane proteinsPreprint

Goverde, C. A., Pačesa, M., Goldbach, N. M., Dornfeld, L., Balbi, P. E. M., Georgeon, S., Rosset, S., Kapoor, S., Choudhury, J., Dauparas, J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.09.540044 · Cited by 20

FAP106 is an interaction hub for assembling microtubule inner proteins at the cilium inner junction

Shimogawa, M. M., Wijono, A. S., Wang, H., Zhang, J., Sha, J., Szombathy, N., Vadakkan, S., Pelayo, P., Jonnalagadda, K., Wohlschlegel, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40230-z · Cited by 18

Spiers Memorial Lecture: How to do impactful research in artificial intelligence for chemistry and materials science

Cheng, A., Ser, C. T., Skreta, M., Guzmán-Cordero, A., Thiede, L., Burger, A., Aldossary, A., Leong, S. X., Pablo‐García, S., Strieth‐Kalthoff, F., et al. (2024) · Faraday Discussions · doi:10.1039/d4fd00153b · Cited by 22

Genome wide structural prediction of ABC transporter systems in Bacillus subtilis

Mahendran, A., & Orlando, B. J. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1469915 · Cited by 20

A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics

Peng, Y., Zhu, J., Wang, S., Liu, Y., Liu, X., DeLeon, O., Zhu, W., Xu, Z., Zhang, X., Zhao, S., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.10.017 · Cited by 21

Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data

Papudeshi, B. N., Roach, M. J., Mallawaarachchi, V., Bouras, G. S., Grigson, S. R., Giles, S. K., Harker, C. M., Hutton, A. L. K., Tarasenko, A. B., Inglis, L. K., et al. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf004 · Cited by 20

Targeted regulation of sterol biosynthesis genes according to perturbations in ergosterol biosynthesis in fungi

Yu, P., Zhou, M., Yu, D., Zhang, Z., Ye, S., Yu, Y., Sun, X., Li, S., & Hu, C. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.01.046 · Cited by 20

Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria

Cacace, E., Tietgen, M., Steinhauer, M., Mateus, A., Schultze, T. G., Eckermann, M., Galardini, M., Varik, V., Koumoutsi, A., Parzeller, J. J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58730-5 · Cited by 20

RBPseg: Toward a complete phage tail fiber structure atlas

Klein-Sousa, V., Roa-Eguiara, A., Kielkopf, C. S., Sofos, N., & Taylor, N. M. I. (2025) · Science Advances · doi:10.1126/sciadv.adv0870 · Cited by 22

Bacteriophage genomes encode both broad and specific counter-defense repertoires to overcome bacterial defense systems

Costa, A. R., van den Berg, D. F., Esser, J. Q., van den Bossche, H., Pozhydaieva, N., Kalogeropoulos, K., & Brouns, S. J. J. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.06.010 · Cited by 18

Of Revolutions and Roadblocks: The Emerging Role of Machine Learning in Biocatalysis

Vornholt, T., Stockinger, P., Mutný, M., Jeschek, M., Nestl, B. M., Oberdorfer, G., Osuna, S., Pleiss, J., Welner, D. H., Krause, A., et al. (2025) · ACS Central Science · doi:10.1021/acscentsci.5c00949 · Cited by 23

AlphaFold2 captures the conformational landscape of the HAMP signaling domain

Winski, A., Ludwiczak, J., Orłowska, M., Madaj, R., Kaminski, K., & Dunin-Horkawicz, S. (2023) · Protein Science · doi:10.1002/pro.4846 · Cited by 18

RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB

Clementel, D., Arrías, P. N., Mozaffari, S., Osmanli, Z., Castro, X. A., curators, R., Borucki, E. L., Cabrera, M., Chinestrad, P., Czarnowski, I., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae965 · Cited by 20

Fast protein structure searching using structure graph embeddings

Greener, J. G., & Jamali, K. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf042 · Cited by 19

The protein structurome of Orthornavirae and its dark matter

Mutz, P., Camargo, A. P., Sahakyan, H., Neri, U., Butković, A., Wolf, Y. I., Krupovìč, M., Dolja, V. V., & Koonin, E. V. (2024) · mBio · doi:10.1128/mbio.03200-24 · Cited by 18

Filamentation activates bacterial Avs5 antiviral protein

Wang, Y., Tian, Y., Yang, X., Yu, F., & Zheng, J. (2025) · Nature Communications · doi:10.1038/s41467-025-57732-7 · Cited by 18

Discovering the nuclear localization signal universe through a deep learning model with interpretable attention units

Li, Y.-F., Pan, X., & Shen, H.-B. (2025) · Patterns · doi:10.1016/j.patter.2025.101262 · Cited by 18

Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body

Chia, M., Ng, A. H. Q., Ravikrishnan, A., Mohamed Naim, A. N., Wearne, S., Common, J., & Nagarajan, N. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02797-4 · Cited by 18

The Role of AI-Driven De Novo Protein Design in the Exploration of the Protein Functional Universe

Zhang, G., Liu, C., Lu, J., Zhang, S., & Zhu, L. (2025) · Biology · doi:10.3390/biology14091268 · Cited by 22

Improved protein binder design using β-pairing targeted RFdiffusion

Sappington, I., Toul, M., Lee, D. S., Robinson, S. A., Goreshnik, I., McCurdy, C., Chan, T. C., Buchholz, N., Huang, B., Vafeados, D. K., et al. (2026) · Nature Communications · doi:10.1038/s41467-025-67866-3 · Cited by 33

The Pseudomonas aeruginosa RpoH (σ32) Regulon and Its Role in Essential Cellular Functions, Starvation Survival, and Antibiotic Tolerance

Williamson, K. S., Dlakić, M., Akiyama, T., & Franklin, M. J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021513 · Cited by 18

Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes

Chen, B., Liu, G., Chen, Q., Wang, H., Liu, L., & Tang, K. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.12.025 · Cited by 18

Novel Secreted Effectors Conserved Among Smut Fungi Contribute to the Virulence of Ustilago maydis

Schuster, M., Schweizer, G., Reißmann, S., Happel, P., Daniela, A., Rössel, N., Güldener, U., Mannhaupt, G., Ludwig, N., Winterberg, S., et al. (2024) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-09-23-0139-fi · Cited by 17

Mriyaviruses: small relatives of giant viruses

Yutin, N., Mutz, P., Krupovic, M., & Koonin, E. V. (2024) · mBio · doi:10.1128/mbio.01035-24 · Cited by 18

Emerging tools and best practices for studying gut microbial community metabolism

Noecker, C. A., & Turnbaugh, P. J. (2024) · Nature Metabolism · doi:10.1038/s42255-024-01074-z · Cited by 20

Phosphorylation of PIP2;7 by CPK28 or Phytophthora kinase effectors dampens pattern-triggered immunity in Arabidopsis

Zhu, H. H., Bao, Y., Peng, H. F., Li, X., Pan, W., Yang, Y., Kuang, Z., Ji, P., Liu, J., Shen, D., et al. (2024) · Plant Communications · doi:10.1016/j.xplc.2024.101135 · Cited by 18

Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor

Lokareddy, R. K., Hou, C.-F. D., Forti, F., Iglesias, S. M., Li, F., Pavlenok, M., Horner, D. S., Niederweis, M., Briani, F., & Cingolani, G. (2024) · Nature Communications · doi:10.1038/s41467-024-52752-1 · Cited by 18

Dual RNA-seq reveals distinct families of co-regulated and structurally conserved effectors in Botrytis cinerea infection of Arabidopsis thaliana

Wei, J., Zhou, Q., Zhang, J., Wu, M., Li, G., & Yang, L. (2024) · BMC Biology · doi:10.1186/s12915-024-02043-4 · Cited by 20

On the possibility of yet a third kinetochore system in the protist phylum Euglenozoa

Benz, C., Raas, M. W. D., Tripathi, P., Faktorová, D., Tromer, E. C., Akiyoshi, B., & Lukeš, J. (2024) · mBio · doi:10.1128/mbio.02936-24 · Cited by 18

Protein structure alignment by Reseek improves sensitivity to remote homologs

Edgar, R. C. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae687 · Cited by 21

Repeated duplications and losses shaped SMC complex evolution from archaeal ancestors to modern eukaryotes

van Hooff, J. J. E., Raas, M. W. D., Tromer, E. C., & Eme, L. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115855 · Cited by 18

Assessing Generative Model Coverage of Protein Structures with SHAPES

Lu, T., Liu, M., Chen, Y., Kim, J., & Huang, P. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101347 · Cited by 18

Predicting phage-bacteria interactions at the strain level from genomesPreprint

Gaborieau, B., Vaysset, H., Tesson, F., Charachon, I., Dib, N., Bernier, J., Dequidt, T., Georjon, H., Clermont, O., Hersen, P., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.22.567924 · Cited by 18

AlphaFold2 structures template ligand discoveryPreprint

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Deciphering direct interspecies electron transfer activity in microbial interactions: The influence of conductive materials in anoxic ecosystems

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