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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Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions

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Silica-associated proteins from hexactinellid sponges support an alternative evolutionary scenario for biomineralization in Porifera

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Widespread horizontal gene transfer between plants and bacteria

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Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses

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Cryo-EM structure of the β-1,3-glucan synthase FKS1-Rho1 complex

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Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls

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CRISPR Screens Identify Toxoplasma Genes That Determine Parasite Fitness in Interferon Gamma-Stimulated Human Cells

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Genomic and phenotypic evolution of nematode-infecting microsporidia

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Structure and electromechanical coupling of a voltage-gated Na+/H+ exchanger

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Discovery of a Thermostable Tagatose 4-Epimerase Powered by Structure- and Sequence-Based Protein Clustering

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Viromics approaches for the study of viral diversity and ecology in microbiomes

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Deep Mutational Scanning of FDX1 Identifies Key Structural Determinants of Lipoylation and Cuproptosis

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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

Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zonePreprint

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The Diverse Evolutionary Histories of Domesticated Metaviral Capsid Genes in Mammals

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Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages

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The vast majority of somatic mutations in plants are layer-specific

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An array of Zymoseptoria tritici effectors suppress plant immune responses

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Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

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New antiviral defences are genetically embedded within prokaryotic immune systemsPreprint

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PINDER: The protein interaction dataset and evaluation resourcePreprint

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The origin, deployment, and evolution of a plant-parasitic nematode effectorome

Molloy, B., Shin, D. S., Long, J., Pellegrin, C., Senatori, B., Vieira, P., Thorpe, P. J., Damm, A., Ahmad, M., Vermeulen, K., et al. (2024) · PLOS Pathogens · doi:10.1371/journal.ppat.1012395 · Cited by 32

Structure-informed protein language models are robust predictors for variant effects

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Taxonomic expansion and reorganization of Flaviviridae

Peter Simmonds, K., Butković, A., Grove, J., Mayne, R., Mifsud, J. C. O., Beer, M., Bukh, J., Drexler, J. F., Kapoor, A., Lohmann, V., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02134-0 · Cited by 43

DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models

Gao, J., Tong, M., Lee, C., Gaertig, J., Legal, T., & Bui, K. H. (2024) · Structure · doi:10.1016/j.str.2024.04.017 · Cited by 29

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors

Varadi, M., Bordin, N., Orengo, C., & Velankar, S. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102543 · Cited by 29

Structural insights into the chloroplast protein import in land plants

Liang, K., Jin, Z., Zhan, X., Li, Y., Xu, Q., Xie, Y., Yang, Y., Wang, S., Wu, J., & Zhen, Y. (2024) · Cell · doi:10.1016/j.cell.2024.08.003 · Cited by 29

Histones and histone variant families in prokaryotes

Schwab, S., Hu, Y., van Erp, B., Cajili, M. K. M., Hartmann, M. D., Alvarez, B. H., Alva, V., Boyle, A. L., & Dame, R. T. (2024) · Nature Communications · doi:10.1038/s41467-024-52337-y · Cited by 32

Use of whole genome sequencing for surveillance and control of foodborne diseases: status quo and quo vadis

Schadron, T., van den Beld, M. J. C., Mughini‐Gras, L., & Franz, E. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1460335 · Cited by 29

A General Substitution Matrix for Structural Phylogenetics

Garg, S. G., & Hochberg, G. K. A. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf124 · Cited by 29

Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

Jha, N., Kravitz, J., West-Roberts, J., Lu, C., Camargo, A. P., Roux, S., Cornman, A., & Hwang, Y. (2025) · Science Advances · doi:10.1126/sciadv.adv5109 · Cited by 36

Foldcomp: a library and format for compressing and indexing large protein structure sets

Kim, H., Mirdita, M., & Steinegger, M. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad153 · Cited by 29

Protein target highlights in CASP15 : Analysis of models by structure providers

Alexander, L. T., Durairaj, J., Kryshtafovych, A., Abriata, L. A., Bayo, Y., Bhabha, G., Breyton, C., Caulton, S. G., Chen, J., Degroux, S., et al. (2023) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26545 · Cited by 28

TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions

Sledzieski, S., Devkota, K., Singh, R., Cowen, L., & Berger, B. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad663 · Cited by 27

Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling

Mutz, P., Resch, W., Faure, G., Senkevich, T. G., Koonin, E. V., & Moss, B. (2023) · mBio · doi:10.1128/mbio.00408-23 · Cited by 26

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Steindorff, A. S., Pontes, M. V. A., Robinson, A., Andreopoulos, B., LaButti, K. M., Kuo, A., Mondo, S. J., Riley, R. W., Otillar, R., Haridas, S., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-06681-w · Cited by 31

Anti-viral defence by an mRNA ADP-ribosyltransferase that blocks translation

Vassallo, C. N., Doering, C. R., & Laub, M. T. (2024) · Nature · doi:10.1038/s41586-024-08102-8 · Cited by 35

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

Drobiazko, A., Adams, M. C., Skutel, M. A., Potekhina, K., Kotovskaya, O., Trofimova, A. B., Matlashov, M. E., Yatselenko, D., Maxwell, K. L., Blower, T. R., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57006-2 · Cited by 31

Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions

Wu, T., Stein, R. A., Kao, T., Brown, B. P., & Mchaourab, H. S. (2025) · Nature Communications · doi:10.1038/s41467-025-62582-4 · Cited by 34

Viro3D: a comprehensive database of virus protein structure predictions

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Identification of the bacteriophage nucleus protein interaction network

Enüstün, E., Deep, A., Gu, Y., Nguyen, K. T., Chaikeeratisak, V., Armbruster, E. G., Ghassemian, M., Villa, E., Pogliano, J., & Corbett, K. D. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01094-5 · Cited by 27

KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein–Protein Interactions to Promote Cancer Cell Survival

Saleh, H., Liloglou, T., Rigden, D. J., Parsons, J. L., & Grundy, G. J. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168434 · Cited by 29

Ultra-fast protein structure prediction to capture effects of sequence variation in mutation moviesPreprint

Weißenow, K., Heinzinger, M., Steinegger, M., & Rost, B. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.14.516473 · Cited by 29

The PDLIM family of actin-associated proteins and their emerging role in membrane trafficking

Healy, M. D., & Collins, B. M. (2023) · Biochemical Society Transactions · doi:10.1042/bst20220804 · Cited by 32

Caspase-1 activates gasdermin A in non-mammals

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Caenorhabditis elegans RIG-I-like receptor DRH-1 signals via CARDs to activate antiviral immunity in intestinal cells

Batachari, L. E., Dai, A. Y., & Troemel, E. R. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2402126121 · Cited by 24

Quest for Orthologs in the Era of Biodiversity Genomics

Langschied, F., Bordin, N., Cosentino, S., Fuentes-Palacios, D., Glover, N., Hiller, M., Hu, Y., Huerta-Cepas, J., Coelho, L. P., Iwasaki, W., et al. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae224 · Cited by 26

AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins

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Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina

Tagirdzhanova, G. M., Scharnagl, K., Sahu, N., Xia, Y., Bucknell, A., Bentham, A. R., Jégousse, C., Ament‐Velásquez, S. L., Brännström, I. O., Johannesson, H., et al. (2025) · Current Biology · doi:10.1016/j.cub.2024.12.041 · Cited by 28

ProtMamba: a homology-aware but alignment-free protein state space model

Sgarbossa, D., Malbranke, C., & Bitbol, A.-F. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf348 · Cited by 27

Computing the Human InteractomePreprint

Zhang, J., Humphreys, I. R., Pei, J., Kim, J., Choi, C., Yuan, R., Durham, J., Liu, S., Choi, H., Baek, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.01.615885 · Cited by 27

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies

Ellaway, J. I. J., Anyango, S., Nair, S. S., Zaki, H. A., Nadzirin, N., Powell, H. R., Gutmanas, A., Váradi, M., & Velankar, S. S. (2024) · Structural Dynamics · doi:10.1063/4.0000251 · Cited by 28

Artificial intelligence-driven computational methods for antibody design and optimization

Vecchietti, L. F., Wijaya, B. N., Armanuly, A., Hangeldiyev, B., Jung, H., Lee, S., Cha, M., & Kim, H. M. (2025) · mAbs · doi:10.1080/19420862.2025.2528902 · Cited by 32

Evidence for a Widespread Third System for Bacterial Polysaccharide Export across the Outer Membrane Comprising a Composite OPX/β-Barrel Translocon

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How AlphaFold2 shaped the structural coverage of the human transmembrane proteome

Jambrich, M. A., Tusnády, G., & Dobson, L. (2023) · Scientific Reports · doi:10.1038/s41598-023-47204-7 · Cited by 27

Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane

Magaña, A. G., Tascón, I., Altuna-Alvarez, J., Queralt-Martín, M., Colautti, J., Velázquez, C., Zabala-Zearreta, M., Rojas-Palomino, J., Cárdenas, M., Alcaraz, A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43585-5 · Cited by 24

Efficient and scalable de novo protein design using a relaxed sequence spacePreprint

Frank, C., Khoshouei, A., de Stigter, Y., Schiewitz, D., Feng, S., Ovchinnikov, S., & Dietz, H. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.24.529906 · Cited by 26

Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder CompetitionPreprint

Cotet, T., Krawczuk, I., Stocco, F., Ferruz, N., Gitter, A., Kurumida, Y., Machado, L. D. A., Paesani, F., Calia, C. N., Challacombe, C. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.17.648362 · Cited by 32

Structure and mechanism of the type I-G CRISPR effector

Shangguan, Q., Graham, S., Sundaramoorthy, R., & White, M. F. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac925 · Cited by 24

Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach

Frey, B., Aiesi, M., Rast, B. M., Rüthi, J., Julmi, J., Stierli, B., Qi, W., & Brunner, I. L. (2024) · PLoS ONE · doi:10.1371/journal.pone.0300503 · Cited by 26

Streptomyces umbrella toxin particles block hyphal growth of competing species

Zhao, Q., Bertolli, S. K., Park, Y., Tan, Y., Cutler, K. J., Srinivas, P., Asfahl, K. L., Garcia, C. F., Gallagher, L. A., Li, Y., et al. (2024) · Nature · doi:10.1038/s41586-024-07298-z · Cited by 26

An essential and highly selective protein import pathway encoded by nucleus-forming phage

Morgan, C. J., Enustun, E., Armbruster, E. G., Birkholz, E. A., Prichard, A., Forman, T., Aindow, A., Wannasrichan, W., Peters, S., Inlow, K., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2321190121 · Cited by 25

Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP

Pulsford, S. B., Outram, M. A., Förster, B., Rhodes, T., Williams, S. J., Badger, M. R., Price, G. D., Jackson, C. J., & Long, B. M. (2024) · Science Advances · doi:10.1126/sciadv.adk7283 · Cited by 25

Structure and replication of Pseudomonas aeruginosa phage JBD30

Valentová, L., Füzik, T., Nováček, J., Hlavenková, Z., Pospíšil, J., & Plevka, P. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00195-1 · Cited by 26

CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy

Wang, T., Li, Z., Xu, K., Huang, W., Huang, G., Zhang, Q. C., & Yan, N. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2417046121 · Cited by 26

Teaching AI to speak protein

Heinzinger, M., & Rost, B. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.102986 · Cited by 27

The E3-ome gene-centric compendium reveals the human E3 ligase landscape

Chua, N. K., González-Robles, T. J., Reddington, C. J., Dudley-Fraser, J., Birkinshaw, R. W., Han, J., Solano, A. N., Wong, S. W., Kochańczyk, T., Peter, J. J., et al. (2026) · Cell · doi:10.1016/j.cell.2026.01.029 · Cited by 29

The prospects and opportunities of protein structure prediction with AI

Tunyasuvunakool, K. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00488-5 · Cited by 25

Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning

Aubel, M., Eicholt, L. A., & Bornberg‐Bauer, E. (2023) · F1000Research · doi:10.12688/f1000research.130443.1 · Cited by 24

Structure of the multi-subunit chloroplast RNA polymerase

do Prado, P. F. V., Ahrens, F. M., Liebers, M., Ditz, N., Braun, H., Pfannschmidt, T., & Hillen, H. S. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.003 · Cited by 27

Cryo-EM structure of flagellotropic bacteriophage Chi

Sonani, R. R., Esteves, N. C., Scharf, B. E., & Egelman, E. H. (2024) · Structure · doi:10.1016/j.str.2024.03.011 · Cited by 24

Intragenomic conflicts with plasmids and chromosomal mobile genetic elements drive the evolution of natural transformation within species

Mazzamurro, F., Chirakadavil, J. B., Durieux, I., Poiré, L., Plantade, J., Ginévra, C., Jarraud, S., Wilharm, G., Charpentier, X., & Rocha, E. P. C. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002814 · Cited by 25

From discovery to application: Enabling technology-based optimizing carbonyl reductases biocatalysis for active pharmaceutical ingredient synthesis

Gu, J., Mu, W., Xu, Y., & Nie, Y. (2024) · Biotechnology Advances · doi:10.1016/j.biotechadv.2024.108496 · Cited by 27

Improved enzyme functional annotation prediction using contrastive learning with structural inference

Yang, Y., Jerger, A., Feng, S., Wang, Z., Brasfield, C., Cheung, M. S., Zucker, J., & Guan, Q. (2024) · Communications Biology · doi:10.1038/s42003-024-07359-z · Cited by 24

Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction

Yue, P., Wu, J., Sun, Y., Zhang, Y., Wang, Q., & Shao, S. (2025) · Nature Communications · doi:10.1038/s41467-025-56526-1 · Cited by 28

Generative AI for the Design of Molecules: Advances and Challenges

Sun, Y., Chen, L., Jing, Z., Li, Y. Y., Kim, D., Gao, J.-Y., Noroozi, R., Yi, G. Y., Feugmo, C. G. T., Klinkova, A., et al. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02234 · Cited by 29

Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches

Lam, J. H., & Katritch, V. (2025) · npj Drug Discovery. · doi:10.1038/s44386-025-00031-4 · Cited by 30

Dockground resource for protein recognition studies

Collins, K. W., Copeland, M. M., Kotthoff, I., Singh, A., Kundrotas, P. J., & Vakser, I. A. (2022) · Protein Science · doi:10.1002/pro.4481 · Cited by 22

Functional annotation of a divergent genome using sequence and structure-based similarity

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Rationally seeded computational protein design of ɑ-helical barrels

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