Fast and accurate protein structure search with Foldseek

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

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

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

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

Accelerated Profile HMM Searches

Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975

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 5,990

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

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,549

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

Buchfink, B., Reuter, K., & Drost, H.-G. (2021) · Nature Methods · doi:10.1038/s41592-021-01101-x · Cited by 5,097

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

Steinegger, M., & Söding, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3988 · Cited by 4,840

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

Zhang, Y. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki524 · Cited by 3,774

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

Shindyalov, I., & Bourne, P. (1998) · Protein Engineering · doi:10.1093/protein/11.9.739 · Cited by 2,199

Explaining Conformational Diversity in Protein Families through Molecular Motions

Lombard, V., Grudinin, S., & Laine, É. (2024) · Scientific Data · doi:10.1038/s41597-024-03524-5 · Cited by 20

Foundation models of protein sequences: A brief overview

Bjerregaard, A., Groth, P. M., Hauberg, S., Krogh, A., & Boomsma, W. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103004 · Cited by 16

Conserved genetic basis for microbial colonization of the gut

Liu, M., Blattman, S. B., Takahashi, M., Nandan, M. O., Jiang, W., Oikonomou, P., Tavazoie, S. F., & Tavazoie, S. (2025) · Cell · doi:10.1016/j.cell.2025.03.010 · Cited by 16

Role of the LuxR solo, SdiA, in eavesdropping on foreign bacteria

Schwieters, A., & Ahmer, B. M. M. (2025) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf015 · Cited by 17

A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people

Welsh, C., Cabotaje, P. R., Marcelino, V. R., Watts, T. D., Kountz, D. J., Jespersen, M., Gould, J. A., Doan, N. Q., Lingford, J. P., Koralegedara, T., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02154-w · Cited by 24

RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity

Dmytrenko, O., Yuan, B., Crosby, K. T., Krebel, M., Chen, X., Nowak, J. S., Chramiec‐Głąbik, A., Filani, B., Gribling-Burrer, A.-S., van der Toorn, W., et al. (2026) · Nature · doi:10.1038/s41586-025-09852-9 · Cited by 18

How artificial intelligence is reengineering protein engineering

Listgarten, J., & Jiang, H. (2026) · Science · doi:10.1126/science.aec8444 · Cited by 20

COLLAPSE : A representation learning framework for identification and characterization of protein structural sites

(2022) · doi:10.1002/pro.4541 · Cited by 16

Foldseek gives AlphaFold protein database a rapid search tool

Hutson, M. (2023) · Nature · doi:10.1038/d41586-023-02205-4 · Cited by 16

Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat

Jost, M., Outram, M. A., Dibley, K. E., Zhang, J., Luo, M., & Ayliffe, M. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1223504 · Cited by 19

The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings

Garin, T., Brin, C., Préveaux, A., Brault, A., Briand, M., Simonin, M., Barret, M., Journet, L., & Sarniguet, A. (2024) · Molecular Plant Pathology · doi:10.1111/mpp.13412 · Cited by 15

Selfish conflict underlies RNA-mediated parent-of-origin effects

Pliota, P., Marvanova, H., Koreshova, A., Kaufman, Y., Tikanova, P., Krogull, D., Hagmüller, A., Widen, S. A., Handler, D., Gokcezade, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07155-z · Cited by 18

Mastigoneme structure reveals insights into the O-linked glycosylation code of native hydroxyproline-rich helices

Dai, J., Ma, M., Niu, Q., Eisert, R. J., Wang, X., Das, P., Lechtreck, K. F., Dutcher, S. K., Zhang, R., & Brown, A. (2024) · Cell · doi:10.1016/j.cell.2024.03.005 · Cited by 16

Identification of domains in Plasmodium falciparum proteins of unknown function using DALI search on AlphaFold predictions

Behrens, H. M., & Spielmann, T. (2024) · Scientific Reports · doi:10.1038/s41598-024-60058-x · Cited by 18

Sequential breakdown of the Cf‐9 leaf mould resistance locus in tomato by Fulvia fulva

de la Rosa, S., Schol, C. R., Peregrina, Á. R., Winter, D. J., Hilgers, A. M., Maeda, K., Iida, Y., Tarallo, M., Jia, R., Beenen, H. G., et al. (2024) · New Phytologist · doi:10.1111/nph.19925 · Cited by 18

Cell-selective proteomics reveal novel effectors secreted by an obligate intracellular bacterial pathogen

Sanderlin, A. G., Margolis, H. K., Meyer, A. F., & Lamason, R. L. (2024) · Nature Communications · doi:10.1038/s41467-024-50493-9 · Cited by 14

Protein engineering in the deep learning era

Zhou, B., Tan, Y., Hu, Y., Zheng, L., Zhong, B., & Hong, L. (2024) · mLife · doi:10.1002/mlf2.12157 · Cited by 18

Persistent mirusvirus infection in the marine protist Aurantiochytrium

Chung, D., Brask, N., Matar, S., Gallot-Lavallée, L., Pringle, E. S., Duguay, B. A., Blais, C., Latimer, J., Haro, R. E., Slamovits, C. H., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65172-6 · Cited by 17

Mining folded proteomes in the era of accurate structure prediction

Bayly-Jones, C., & Whisstock, J. C. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009930 · Cited by 16

Giant genes are rare but implicated in cell wall degradation by predatory bacteriaPreprint

West-Roberts, J. A., Valentin-Alvarado, L. E., Mullen, S., Sachdeva, R., Smith, J., Hug, L. A., Grégoire, D. S., Liu, W., Lin, T., Husain, G., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.21.568195 · Cited by 16

Computational design of serine hydrolases

Lauko, A., Pellock, S. J., Anischanka, I., Sumida, K. H., Juergens, D., Ahern, W., Shida, A., Hunt, A., Kalvet, I., Norn, C., et al. (2024) · doi:10.1101/2024.08.29.610411 · Cited by 16

Naringenin chalcone carbon double-bond reductases mediate dihydrochalcone biosynthesis in apple leaves

Yauk, Y., Dare, A. P., Cooney, J. M., Wang, Y., Hamiaux, C., McGhie, T. K., Wang, M., Li, P., & Atkinson, R. G. (2024) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiae515 · Cited by 15

ProtSpace: A Tool for Visualizing Protein Space

Senoner, T., Olenyi, T., Heinzinger, M., Spannagl, A., Bouras, G. S., Rost, B., & Koludarov, I. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.168940 · Cited by 17

Quorum Sensing Coordinates Carbon and Nitrogen Metabolism to Optimize Public Goods Production in Pseudomonas fluorescens 2P24

Li, J., Nie, M., Ma, H., Tao, X., Sun, Y., Tu, X., Zhang, P., Zhang, L., Jia, R. L., He, Y., et al. (2025) · Advanced Science · doi:10.1002/advs.202412224 · Cited by 16

Comparison of cable bacteria genera reveals details of their conduction machinery

Digel, L., Justesen, M. L., Madsen, N. S., Fransaert, N., Wouters, K., Bonné, R., Plum-Jensen, L. E., Marshall, I. P. G., Jensen, P. B., Nicolas-Asselineau, L., et al. (2025) · EMBO Reports · doi:10.1038/s44319-025-00387-8 · Cited by 16

Phytopathogen Effector Biology in the Burgeoning AI Era

Jones, D., & Raffaele, S. (2025) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-121823-081033 · Cited by 17

A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align

Zhang, C., Freddolino, L., & Zhang, Y. (2025) · Nature Protocols · doi:10.1038/s41596-025-01189-x · Cited by 17

Functional RNA splitting drove the evolutionary emergence of type V CRISPR-Cas systems from transposons

Jin, S., Zhu, Z., Li, Y., Zhang, S., Liu, Y., Li, D., Li, Y., Luo, Y., Cheng, Z., Zhao, K. T., et al. (2025) · Cell · doi:10.1016/j.cell.2025.09.004 · Cited by 16

Cenote-Taker 3 for fast and accurate virus discovery and annotation of the virome

Tisza, M. J., Varsani, A., Petrosino, J. F., & Cregeen, S. J. (2026) · Peer Community Journal · doi:10.24072/pcjournal.706 · Cited by 25

To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units

Kryshtafovych, A., & Rigden, D. J. (2023) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26533 · Cited by 14

Moving toward a better understanding of the model bacterial predator Bdellovibrio bacteriovorus

Caulton, S. G., & Lovering, A. L. (2023) · Microbiology · doi:10.1099/mic.0.001380 · Cited by 15

Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems

Nicastro, G. G., Burroughs, A. M., Iyer, L. M., & Aravind, L. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad879 · Cited by 16

Protein engineering using circular permutation – structure, function, stability, and applications

Das, D., & Ainavarapu, S. R. K. (2024) · FEBS Journal · doi:10.1111/febs.17146 · Cited by 16

Specificity of DNA ADP-Ribosylation Reversal by NADARs

Cihlova, B., Lu, Y., Mikoč, A., Schuller, M., & Ahel, I. (2024) · Toxins · doi:10.3390/toxins16050208 · Cited by 14

Bridging the Gap between Sequence and Structure Classifications of Proteins with AlphaFold Models

Pei, J., Andreeva, A. E., Chuguransky, S., Pinto, B. L., Paysan‐Lafosse, T., Schaeffer, R. D., Bateman, A. G., Cong, Q., & Grishin, N. V. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168764 · Cited by 15

Structure of a Rhs effector clade domain provides mechanistic insights into type VI secretion system toxin delivery

Hayes, B. K., Harper, M., Venugopal, H., Lewis, J. M., Wright, A., Lee, H.-C., Steele, J. R., Steer, D. L., Schittenhelm, R. B., Boyce, J. D., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52950-x · Cited by 15

T6SS-associated Rhs toxin-encapsulating shells: Structural and bioinformatical insights into bacterial weaponry and self-protection

Kielkopf, C. S., Shneider, M. M., Leiman, P. G., & Taylor, N. M. I. (2024) · Structure · doi:10.1016/j.str.2024.10.008 · Cited by 15

Lake salinization on the Qinghai–Tibetan Plateau alters viral community composition and lifestyles

Xie, Y.-G., Qi, Y.-L., Luo, Z., Qu, Y.-N., Yang, J., Liu, S., Yang, H., Xie, D.-W., Wang, Z., Jiang, H., et al. (2025) · Communications Earth & Environment · doi:10.1038/s43247-025-02037-2 · Cited by 14

Activating the d -Tagatose Production Capacity of Escherichia coli with Structural Insights into C4 Epimerase Specificity

Palur, D. S. K., Taylor, J. E., Luu, B., Anderson, I. C., Arredondo, A., Gannalo, T., Skorka, B. A., Denish, P. R., Didzbalis, J., Siegel, J. B., et al. (2025) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.4c12842 · Cited by 14

In silico evolution of globular protein folds from random sequences

Sahakyan, H., Babajanyan, S. G., Wolf, Y. I., & Koonin, E. V. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2509015122 · Cited by 15

Predicting the structural impact of human alternative splicing

Song, Y., Zhang, C., Omenn, G. S., O’Meara, M. J., & Welch, J. D. (2025) · Genome biology · doi:10.1186/s13059-025-03744-x · Cited by 16

An evolutionarily conserved bimodular domain anchors ZC3HC1 and its yeast homologue Pml39p to the nuclear basket

Gunkel, P., Iino, H., Krull, S., & Cordes, V. C. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-09-0402 · Cited by 14

AF2BIND: Predicting ligand-binding sites using the pair representation of AlphaFold2Preprint

Gazizov, A., Lian, A., Goverde, C. A., Ovchinnikov, S., & Polizzi, N. F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.15.562410 · Cited by 15

Novel genomic approaches support Xenacoelomorpha as sister to all BilateriaPreprint

Álvarez‐Presas, M., Ruiz‐Trillo, I., & Paps, J. (2024) · Research Square · doi:10.21203/rs.3.rs-5529390/v1 · Cited by 12

Diverse genetic contexts of HicA toxin domains propose a role in anti-phage defense

Gerdes, K. (2024) · mBio · doi:10.1128/mbio.03293-23 · Cited by 14

From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model

Tan, Y., Wang, R.-L., Wu, B., Hong, L., & Zhou, B. (2025) · Bioinform. · doi:10.1093/bioinformatics/btaf189 · Cited by 25

Transposons and accessory genes drive adaptation in a clonally evolving fungal pathogen

López‐Díaz, C., Ayhan, D. H., López, A. R., Gómez-Gil, L., Ma, L., & Pietro, A. D. (2025) · Nature Communications · doi:10.1038/s41467-025-62213-y · Cited by 16

AI sheds new light on genome editing

Qin, Z. S., Deng, Z., Li, C., Wang, D., Ji, X., & Chen, Z. (2025) · Trends in biotechnology · doi:10.1016/j.tibtech.2025.07.011 · Cited by 15

Computational function prediction of bacteria and phage proteins

Grigson, S. R., Bouras, G. S., Dutilh, B. E., Olson, R., & Edwards, R. A. (2025) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00022-25 · Cited by 18

Multi-dimensional metagenomics

Peng, H., Ruiz-Moreno, A. J., & Fu, J. (2025) · Nature Reviews Bioengineering · doi:10.1038/s44222-025-00346-x · Cited by 19

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Fiamenghi, M. B., Camargo, A. P., Chasapi, I. N., Baltoumas, F. A., Roux, S., Egorov, A. A., Aplakidou, E., Ndela, É. O., Vasquez, Y. M., Chen, I.-M. A., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1283 · Cited by 16

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2

Gazizov, A., Lian, A., Goverde, C. A., Mou, J., Ovchinnikov, S., & Polizzi, N. F. (2026) · Nature Methods · doi:10.1038/s41592-026-03011-2 · Cited by 36

Unanticipated broad phylogeny of BEN DNA-binding domains revealed by structural homology searches

Pan, A., Zeng, Y., Liu, J., Zhou, M., Lai, E. C., & Yu, Y. (2023) · Current Biology · doi:10.1016/j.cub.2023.05.011 · Cited by 14

Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics

Arikawa, K., & Hosokawa, M. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.010 · Cited by 13

Identification of an antivirulence agent targeting the master regulator of virulence genes in Staphylococcus aureus

Arya, R., Kim, T., Youn, J. W., Bae, T., & Kim, K. K. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1268044 · Cited by 13

Emergence of an Orphan Nitrogenase Protein Following Atmospheric Oxygenation

Cuevas-Zuviría, B., Garcia, A. K., Rivier, A. J., Rucker, H. R., Carruthers, B. M., & Kaçar, B. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae067 · Cited by 14

Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination

Tran, N. T., & Le, T. B. K. (2024) · Nature Communications · doi:10.1038/s41467-024-49114-2 · Cited by 15

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Schoelmerich, M. C., Ly, L., West-Roberts, J., Shi, L.-D., Shen, C., Malvankar, N. S., Taib, N., Gribaldo, S., Woodcroft, B. J., Schadt, C. W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49548-8 · Cited by 14

Sequence, Structure, and Functional Space of Drosophila De Novo Proteins

Middendorf, L., Iyengar, B. R., & Eicholt, L. A. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae176 · Cited by 15

New insights into RNA mycoviruses of fungal pathogens causing Fusarium head blight

Buivydaitė, Ž., Winding, A., Jørgensen, L. N., Zervas, A., & Sapkota, R. (2024) · Virus Research · doi:10.1016/j.virusres.2024.199462 · Cited by 14

The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell

Andreas, M. P., & Giessen, T. W. (2024) · Nature Communications · doi:10.1038/s41467-024-54175-4 · Cited by 14

Structural characterization of the full-length Hantaan virus polymerase

Keown, J. R., Carrique, L., Nilsson-Payant, B. E., Fodor, E., & Grimes, J. M. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012781 · Cited by 13

Improving AlphaFold2 ‐ and AlphaFold3 ‐Based Protein Complex Structure Prediction With MULTICOM4 in CASP16

Liu, J., Neupane, P., & Cheng, J. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26850 · Cited by 18

Large language models transform biological research: from architecture to utilization

Wang, T., & Luo, Z. (2025) · Science China Information Sciences · doi:10.1007/s11432-024-4466-3 · Cited by 14

Light-directed evolution of dynamic, multi-state, and computational protein functionalities

Gligorovski, V., Labagnara, M., Scutteri, L., Blackholm, M., Möglich, A., Mansouri, N., & Rahi, S. J. (2026) · Cell · doi:10.1016/j.cell.2026.02.002 · Cited by 13

Programmable design of functional proteins from natural languagePreprint

Dai, F.-Y., You, S.-Y., Zhu, Y.-D., Gao, Y., Fu, L.-H., Zhou, X.-B., Su, J., Wang, C.-T., Fan, Y.-L., Tan, Q.-S., et al. (2026) · bioRxiv · doi:10.1101/2024.08.01.606258 · Cited by 30

Metagenomic-Scale Analysis of the Predicted Protein Structure UniversePreprint

Yeo, J., Han, Y., Bordin, N., Lau, A. M., Kandathil, S. M., Kim, H., Karin, E. L., Mirdita, M., Jones, D. T., Orengo, C. A., et al. (2025) · SSRN Electronic Journal · doi:10.1101/2025.04.23.650224 · Cited by 16

Understanding Language Model Scaling on Protein Fitness PredictionPreprint

Hou, C., Liu, D., Zafar, A., & Shen, Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.25.650688 · Cited by 14

Mapping the ultrastructural topology of the corynebacterial cell surface

Isbilir, B., Yeates, A., Alva, V., & Bharat, T. A. M. (2025) · PLOS Biology · doi:10.1371/journal.pbio.3003130 · Cited by 18

Haplotyped genome mapping and functional characterization of a blueberry anthocyanin acetyltransferase (AAT) controlling the accumulation of acylated anthocyanins

Dare, A. P., Wu, C., Carvajal, J. I., Nguyen, H. M., Günther, C. S., Hamiaux, C., Bailey, S., Deng, C. H., Mengist, M. F., Iorizzo, M., et al. (2024) · Journal of Experimental Botany · doi:10.1093/jxb/erae489 · Cited by 14

Structure of Mycobacterial NDH-2 Bound to a 2-Mercapto-Quinazolinone Inhibitor

Liang, Y., Bueler, S. A., Cook, G. M., & Rubinstein, J. L. (2025) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5c00049 · Cited by 13

Structure and assembly of the MmpL5/MmpS5 efflux transporter from Mycobacterium tuberculosis

Xiong, Z., Yang, X., Wang, S., Smart, C. J., Sisson, H. M., Lin, Z., Hu, T., Ran, Y., Xu, C., Yang, X., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60365-5 · Cited by 13

Tokenized and continuous embedding compressions of protein sequence and structure

Lu, A. X., Yan, W., Yang, K. K., Gligorijević, V., Cho, K., Abbeel, P., Bonneau, R., & Frey, N. C. (2025) · Patterns · doi:10.1016/j.patter.2025.101289 · Cited by 17

NAD-dependent dehydrogenases enable efficient growth of Paracoccus denitrificans on the PET monomer ethylene glycol

Ren, M., Li, D., Addison, H., Noteborn, W. E. M., Andeweg, E. H., Glatter, T., de Winde, J. H., Rebelein, J. G., Lamers, M. H., & von Borzyskowski, L. S. (2025) · Nature Communications · doi:10.1038/s41467-025-61056-x · Cited by 15

Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex

Lupton, C. J., Bayly-Jones, C., Dong, S., Lam, T., Luo, W., Jones, G. D., Mastos, C., Frescher, N. J., Lim, S. S., Keen, A. C., et al. (2026) · Cell · doi:10.1016/j.cell.2025.12.005 · Cited by 15

Emergence and evolution of protein-coding de novo genes

Bornberg‐Bauer, E., & Eicholt, L. A. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-025-00929-9 · Cited by 15

Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia

Karakurt, S., Johnson, D. R., Fenner, K., & Hafner, J. (2023) · Water Research · doi:10.1016/j.watres.2023.120756 · Cited by 13

Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure

Corum, M. R., Venkannagari, H., Hryc, C. F., & Baker, M. L. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.01.021 · Cited by 15

CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA

Bell, R. T., Sahakyan, H., Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2024) · eLife · doi:10.7554/elife.94800.3 · Cited by 3

Stepwise assembly and release of Tc toxins from Yersinia entomophaga

Feldmüller, M., Ericson, C. F., Afanasyev, P., Lien, Y., Weiss, G. L., Wollweber, F., Schoof, M., Hurst, M., & Pilhofer, M. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01611-2 · Cited by 14

Fungtion: A Server for Predicting and Visualizing Fungal Effector Proteins

Li, J., Ren, J., Dai, W., Stubenrauch, C. J., Finn, R. D., & Wang, J. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168613 · Cited by 13

The inorganic pyrophosphatases of microorganisms: a structural and functional review

García‐Contreras, R., de la Mora, J., Mora-Montes, H. M., Martínez-Álvarez, J. A., Vicente-Gómez, M., Padilla‐Vaca, F., Vargas-Maya, N. I., & Franco, B. (2024) · PeerJ · doi:10.7717/peerj.17496 · Cited by 13

Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models

Cuturello, F., Celoria, M., Ansuini, A., & Cazzaniga, A. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae447 · Cited by 11

A survey of the Desulfuromonadia “cytochromome” provides a glimpse of the unexplored diversity of multiheme cytochromes in nature

Soares, R., Fonseca, B. M., Nash, B. W., Paquete, C. M., & Louro, R. O. (2024) · BMC Genomics · doi:10.1186/s12864-024-10872-4 · Cited by 13

Identification of new SdiA regulon members of Escherichia coli , Enterobacter cloacae , and Salmonella enterica serovars Typhimurium and Typhi

Schwieters, A., & Ahmer, B. M. M. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.01929-24 · Cited by 13

Enhanced prediction of protein functional identity through the integration of sequence and structural features

Fujita, S., & Terada, T. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.11.028 · Cited by 13

Learning a generalized graph transformer for protein function prediction in dissimilar sequences

Fu, Y., Gu, Z., Luo, X., Guo, Q., Lai, L., & Deng, M. (2024) · GigaScience · doi:10.1093/gigascience/giae093 · Cited by 12

A typical NLR recognizes a family of structurally conserved effectors to confer plant resistance against adapted and non-adapted Phytophthora pathogens

Dong, X., Xu, L., Zhu, H., Zhu, Z., Ji, P., Li, X., Li, T., Zhang, X., Ai, G., & Dou, D. (2025) · Molecular Plant · doi:10.1016/j.molp.2025.01.018 · Cited by 12

Enzymatic peptide macrocyclization via indole- N -acylation

Maruyama, H., Yamada, Y., Igarashi, Y., Matsuda, K., & Wakimoto, T. (2025) · Chemical Science · doi:10.1039/d4sc07839j · Cited by 13

Barlow Twins deep neural network for advanced 1D drug–target interaction prediction

Schuh, M. G., Boldini, D., Bohne, A. I., & Sieber, S. A. (2025) · Journal of Cheminformatics · doi:10.1186/s13321-025-00952-2 · Cited by 13

Extensive and diverse lanthanide-dependent metabolism in the ocean

Voutsinos, M. Y., Banfield, J. F., & McClelland, H. L. O. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf057 · Cited by 14

AlphaFold2's training set powers its predictions of some fold‐switched conformations

Schafer, J. W., & Porter, L. L. (2025) · Protein Science · doi:10.1002/pro.70105 · Cited by 12

Mystique, a broad host range Acinetobacter phage, reveals the impact of culturing conditions on phage isolation and infectivity

Alseth, E., Roush, C., Irby, I., Kopylov, M., Bobe, D., Diggs, M. W., Nguyen, K., Xu, H., Schmidt‐Krey, I., Bryksin, A. V., et al. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1012986 · Cited by 14

Molecular basis for the assembly of the Vps5-Vps17 SNX-BAR proteins with Retromer

Chen, K.-E., Tillu, V. A., Gopaldass, N., Chowdhury, S. R., Leneva, N., Kovtun, O., Ruan, J., Guo, Q., Ariotti, N., Mayer, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58846-8 · Cited by 13

Aboral cell types of Clytia and coral larvae have shared features and link taurine to the regulation of settlement

Ramon-Mateu, J., Ferraioli, A., Teixidó, N., Domart-Coulon, I. J., Houliston, E., & Copley, R. R. (2025) · Science Advances · doi:10.1126/sciadv.adv1159 · Cited by 15

Unveiling the evolution of antimicrobial peptides in gut microbes via foundation-model-powered framework

Li, W., Huang, B., Guo, M., Zeng, Z., Cai, T., Feng, L., Zhang, X., Guo, L., Jiang, X., Yin, Y., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115773 · Cited by 13

A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1

Koszela, J., Rintala-Dempsey, A., Salzano, G., Pimenta, V., Kamarainen, O., Gabrielsen, M., Parui, A. L., Shaw, G. S., & Walden, H. (2025) · Journal of Cell Biology · doi:10.1083/jcb.202408025 · Cited by 13

Newly Developed Structure-Based Methods Do Not Outperform Standard Sequence-Based Methods for Large-Scale Phylogenomics

Mutti, G., Ocaña‐Pallarès, E., & Gabaldón, T. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf149 · Cited by 13

PepPCBench is a Comprehensive Benchmarking Framework for Protein–Peptide Complex Structure Prediction

Zhai, S., Zhao, H., Wang, J., Lin, S., Liu, T., Gu, S., Jiang, D., Liu, H., Kang, Y., Yao, X., et al. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01084 · Cited by 21

Donor strand complementation and calcium ion coordination drive the chaperone-free polymerization of archaeal cannulae

Sleutel, M., Sonani, R. R., Miller, J., Wang, F., Socorro, A. G., Chen, Y., Martin, R., Demeler, B., Rudolph, M. J., Alva, V., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64120-8 · Cited by 11

Fast methods for protein structure comparison

van Kempen, M. (2026) · doi:10.53846/goediss-12166

Rich structure alphabets enable highest accuracy protein searchPreprint

Edgar, R. C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.24.740611

TM-search: An Efficient and Effective Tool for Protein Structure Database Search

Liu, Z., Zhang, C., Zhang, Q., Zhang, Y., & Yu, D. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01455 · Cited by 10

Foldseek gives AlphaFold protein database a rapid search tool

Hutson, M. (2023) · Nature · doi:10.1038/d41586-023-02205-4 · Cited by 16

Protein structure alignment by Reseek improves sensitivity to remote homologs

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