Using Dali for Protein Structure Comparison

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320

Protein Structure Comparison by Alignment of Distance Matrices

Holm, L., & Sander, C. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1489 · Cited by 3,984

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

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

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

AlphaFill: enriching AlphaFold models with ligands and cofactors

Hekkelman, M. L., de Vries, I., Joosten, R. P., & Perrakis, A. (2023) · Nature Methods · doi:10.1038/s41592-022-01685-y · Cited by 511

Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease

Karvelis, T., Druteika, G., Bigelyte, G., Budre, K., Zedaveinyte, R., Silanskas, A., Kazlauskas, D., Venclovas, Č., & Siksnys, V. (2021) · Nature · doi:10.1038/s41586-021-04058-1 · Cited by 348

SARM1 is a metabolic sensor activated by an increased NMN/NAD+ ratio to trigger axon degeneration

Figley, M. D., Gu, W., Nanson, J. D., Shi, Y., Sasaki, Y., Cunnea, K., Malde, A. K., Jia, X., Luo, Z., Saikot, F. K., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.02.009 · Cited by 324

A wheat resistosome defines common principles of immune receptor channels

Förderer, A., Li, E., Lawson, A. W., Deng, Y.-N., Sun, Y., Logemann, E., Zhang, X., Wen, J., Han, Z., Chang, J., et al. (2022) · Nature · doi:10.1038/s41586-022-05231-w · Cited by 296

Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein

(2020) · doi:10.1073/pnas.2021785118 · Cited by 274

FATCAT 2.0: towards a better understanding of the structural diversity of proteins

Li, Z., Jaroszewski, L., Iyer, M., Sedova, M., & Godzik, A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa443 · Cited by 231

PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

Liu, W., Wang, Z., You, R., Xie, C., Wei, H., Xiong, Y., Yang, J., & Zhu, S. (2024) · Nature Communications · doi:10.1038/s41467-024-46808-5 · Cited by 96

Predicting protein-protein interactions in the human proteome

Zhang, J., Humphreys, I. R., Pei, J., Kim, J., Choi, C., Yuan, R., Durham, J., Liu, S., Choi, H.-J., Baek, M., et al. (2025) · Science · doi:10.1126/science.adt1630 · Cited by 87

Structure of SARS-CoV-2 M protein in lipid nanodiscs

Dolan, K. A., Dutta, M., Kern, D. M., Kotecha, A., Voth, G. A., & Brohawn, S. G. (2022) · eLife · doi:10.7554/elife.81702 · Cited by 82

Novel machine learning approaches revolutionize protein knowledge

Bordin, N., Dallago, C., Heinzinger, M., Kim, S., Littmann, M., Rauer, C., Steinegger, M., Rost, B., & Orengo, C. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2022.11.001 · Cited by 72

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times

Wang, F., Chan, C. H., Suciu, V., Mustafa, K., Ammend, M., Si, D., Hochbaum, A. I., Egelman, E. H., & Bond, D. R. (2022) · eLife · doi:10.7554/elife.81551 · Cited by 69

Structural basis for host recognition and superinfection exclusion by bacteriophage T5

van den Berg, B., Silale, A., Baslé, A., Brandner, A. F., Mader, S. L., & Khalid, S. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2211672119 · Cited by 53

The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Rocafort, M., Bowen, J. K., Hassing, B., Cox, M. P., McGreal, B., de la Rosa, S., Plummer, K. M., Bradshaw, R. E., & Mesarich, C. H. (2022) · BMC Biology · doi:10.1186/s12915-022-01442-9 · Cited by 52

Biosynthesis of Macrocyclic Peptides with C‑Terminal β‑Amino-α-keto Acid Groups by Three Different Metalloenzymes

Nguyen, D. T., Zhu, L., Gray, D. L., Woods, T. J., Padhi, C., Flatt, K. M., Mitchell, D. A., & van der Donk, W. A. (2024) · ACS Central Science · doi:10.1021/acscentsci.4c00088 · Cited by 51

DeepTracer-ID: De novo protein identification from cryo-EM maps

Chang, L., Wang, F., Connolly, K., Meng, H., Su, Z., Cvirkaite-Krupovic, V., Krupovic, M., Egelman, E. H., & Si, D. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.06.025 · Cited by 50

Structure of the human heparan sulfate polymerase complex EXT1-EXT2

Leisico, F., Omeiri, J., Le Narvor, C., Beaudouin, J., Hons, M., Fenel, D., Schoehn, G., Couté, Y., Bonnaffé, D., Sadir, R., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34882-6 · Cited by 45

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

(2022) · doi:10.1038/s41467-022-31564-1 · Cited by 45

Antibacterial T6SS effectors with a VRR-Nuc domain are structure-specific nucleases

Hespanhol, J. T., Sanchez-Limache, D. E., Nicastro, G. G., Mead, L., Llontop, E. E., Chagas-Santos, G., Farah, C. S., de Souza, R. F., Galhardo, R. D. S., Lovering, A. L., et al. (2022) · eLife · doi:10.7554/elife.82437 · Cited by 45

Total In Vitro Biosynthesis of the Thioamitide Thioholgamide and Investigation of the Pathway

Sikandar, A., Lopatniuk, M., Luzhetskyy, A., Müller, R., & Koehnke, J. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c00402 · Cited by 39

A wheat resistosome defines common principles of immune receptor channels

Förderer, A., Li, E., Lawson, A., Deng, Y.-N., Sun, Y., Logemann, E., Zhang, X., Wen, J., Han, Z., Chang, J., et al. (2022) · doi:10.1101/2022.03.23.485489 · Cited by 36

Dual Targeting Factors Are Required for LXG Toxin Export by the Bacterial Type VIIb Secretion System

(2022) · doi:10.1128/mbio.02137-22 · Cited by 36

Ferric reductase-related proteins mediate fungal heme acquisition

Roy, U., Yaish, S., Weissman, Z., Pinsky, M., Dey, S., Horev, G., & Kornitzer, D. (2022) · eLife · doi:10.7554/elife.80604 · Cited by 32

Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex

Kayastha, K., Katsyv, A., Himmrich, C., Welsch, S., Schuller, J. M., Ermler, U., & Müller, V. (2022) · eLife · doi:10.7554/elife.77095 · Cited by 31

Structural screens identify candidate human homologs of insect chemoreceptors and cryptic Drosophila gustatory receptor-like proteins

(2023) · doi:10.7554/elife.85537 · Cited by 28

Structure of a tripartite protein complex that targets toxins to the type VII secretion system

Klein, T. A., Shah, P. Y., Gkragkopoulou, P., Grebenc, D. W., Kim, Y., & Whitney, J. C. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2312455121 · Cited by 28

Structural Predictions of the SNX-RGS Proteins Suggest They Belong to a New Class of Lipid Transfer Proteins

Paul, B., Weeratunga, S., Tillu, V. A., Hariri, H., Henne, W. M., & Collins, B. M. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.826688 · Cited by 27

A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex

Huene, A. L., Sanders, S. M., Ma, Z., Nguyen, A.-D., Koren, S., Michaca, M. H., Mullikin, J. C., Phillippy, A. M., Schnitzler, C. E., Baxevanis, A. D., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207374119 · Cited by 27

Tryptophan C-mannosylation is critical for Plasmodium falciparum transmission

Lopaticki, S., McConville, R., John, A., Geoghegan, N., Mohamed, S. D., Verzier, L., Steel, R. W. J., Evelyn, C., O’Neill, M. T., Soler, N. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32076-8 · Cited by 26

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

Co-component signal transduction systems: Fast-evolving virulence regulation cassettes discovered in enteric bacteria

(2022) · doi:10.1073/pnas.2203176119 · Cited by 25

Gene amplifications cause high-level resistance against albicidin in gram-negative bacteria

Saathoff, M., Kosol, S., Semmler, T., Tedin, K., Dimos, N., Kupke, J., Seidel, M., Ghazisaeedi, F., Jonske, M. C., Wolf, S. A., et al. (2023) · PLOS Biology · doi:10.1371/journal.pbio.3002186 · Cited by 25

Discovery of archaeal Fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

Moi, D., Nishio, S., Li, X., Valansi, C., Langleib, M., Brukman, N. G., Flyak, K., Dessimoz, C., de Sanctis, D., Tunyasuvunakool, K., et al. (2021) · doi:10.1101/2021.10.13.464100 · Cited by 23

Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine

Kimura, S., Srisuknimit, V., McCarty, K. L., Dedon, P. C., Kranzusch, P. J., & Waldor, M. K. (2022) · Nature Communications · doi:10.1038/s41467-022-33714-x · Cited by 23

Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life

Himmel, N. J., Moi, D., & Benton, R. (2023) · Current Biology · doi:10.1016/j.cub.2023.10.008 · Cited by 23

Redβ177 annealase structure reveals details of oligomerization and λ Red-mediated homologous DNA recombination

Newing, T. P., Brewster, J. L., Fitschen, L. J., Bouwer, J. C., Johnston, N. P., Yu, H., & Tolun, G. (2022) · Nature Communications · doi:10.1038/s41467-022-33090-6 · Cited by 22

How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters

Graham, J. E., Niks, D., Zane, G. M., Gui, Q., Hom, K., Hille, R., Wall, J. D., & Raman, C. S. (2022) · ACS Catalysis · doi:10.1021/acscatal.2c00316 · 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

Fast protein structure searching using structure graph embeddings

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

Neprosin belongs to a new family of glutamic peptidase based on in silico evidence

Ting, T.-Y., Baharin, A., Ramzi, A. B., Ng, C.-L., & Goh, H.-H. (2022) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2022.04.027 · Cited by 17

Biochemical characterisation of Mer3 helicase interactions and the protection of meiotic recombination intermediates

Altmannova, V., Firlej, M., Müller, F., Janning, P., Rauleder, R., Rousova, D., Schäffler, A., Bange, T., & Weir, J. R. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad175 · Cited by 15

AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein

Cummins, M. C., Jacobs, T. M., Teets, F. D., DiMaio, F., Tripathy, A., & Kuhlman, B. (2022) · Protein Science · doi:10.1002/pro.4368 · Cited by 15

Plant-on-chip: Core morphogenesis processes in the tiny plant Wolffia australiana

Li, F., Yang, J.-J., Sun, Z.-Y., Wang, L., Qi, L.-Y., A, S., Liu, Y.-Q., Zhang, H.-M., Dang, L.-F., Wang, S.-J., et al. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgad141 · Cited by 15

Structural basis of microtubule-mediated signal transduction

Choi, S. R., Blum, T. B., Giono, M., Roy, B., Vakonakis, I., Schmid, D., Oelgarth, N., Ranganathan, A., Gossert, A. D., Shivashankar, G. V., et al. (2026) · Cell · doi:10.1016/j.cell.2025.11.011 · Cited by 14

The structure of a Plasmodium vivax Tryptophan Rich Antigen domain suggests a lipid binding function for a pan-Plasmodium multi-gene family

Kundu, P., Naskar, D., McKie, S. J., Dass, S., Kanjee, U., Introini, V., Ferreira, M. U., Cicuta, P., Duraisingh, M., Deane, J. E., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40885-8 · Cited by 14

An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense

Bullen, N. P., Johnson, C. N., Andersen, S. E., Arya, G., Marotta, S. R., Lee, Y.-J., Weigele, P. R., Whitney, J. C., & Duerkop, B. A. (2024) · Nature Communications · doi:10.1038/s41467-024-51346-1 · Cited by 13

A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

Newman, K. E., Tindall, S. N., Mader, S. L., Khalid, S., Thomas, G. H., & Van Der Woude, M. W. (2023) · eLife · doi:10.7554/elife.81547 · Cited by 12

Non-canonical Staphylococcus aureus pathogenicity island repression

Miguel-Romero, L., Alqasmi, M., Bacarizo, J., Tan, J. A., Cogdell, R. J., Chen, J., Byron, O., Christie, G. E., Marina, A., & Penadés, J. R. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac855 · Cited by 9

Systematic identification of Salmonella T6SS effectors uncovers diverse new families and lipid-targeting activities

Nicastro, G. G., Sibinelli-Sousa, S., Hespanhol, J. T., Santos, T. W. C., Munoz, J. P., Santos, R. S., Perez-Sepulveda, B. M., Miyamoto, S., Aravind, L., de Souza, R. F., et al. (2026) · PLOS Biology · doi:10.1371/journal.pbio.3003680 · Cited by 9

The Streptomyces viridochromogenes product template domain represents an evolutionary intermediate between dehydratase and aldol cyclase of type I polyketide synthases

Feng, Y., Yang, X., Ji, H., Deng, Z., Lin, S., & Zheng, J. (2022) · Communications Biology · doi:10.1038/s42003-022-03477-8 · Cited by 9

Refining the domain architecture model of the replication origin firing factor Treslin/TICRR

Ferreira, P., Sanchez-Pulido, L., Marko, A., Ponting, C. P., & Boos, D. (2022) · Life Science Alliance · doi:10.26508/lsa.202101088 · Cited by 9

Multi-conflict islands are a widespread trend within Serratia spp.

Cummins, T., Songra, S., Garrett, S. R., Blower, T. R., & Mariano, G. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.115055 · Cited by 8

The crystal structure of vaccinia virus protein E2 and perspectives on the prediction of novel viral protein folds

(2022) · doi:10.1099/jgv.0.001716 · Cited by 8

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

(2025) · doi:10.1128/spectrum.02871-24 · Cited by 8

Structural Insights into the Dimeric Form of Bacillus subtilis RNase Y Using NMR and AlphaFold

Morellet, N., Hardouin, P., Assrir, N., van Heijenoort, C., & Golinelli-Pimpaneau, B. (2022) · Biomolecules · doi:10.3390/biom12121798 · Cited by 7

The structural basis for deubiquitination by the fingerless USP-type effector TssM

Hermanns, T., Uthoff, M., Baumann, U., & Hofmann, K. (2024) · Life Science Alliance · doi:10.26508/lsa.202302422 · Cited by 7

A novel family of sugar-specific phosphodiesterases that remove zwitterionic modifications of GlcNAc

Fossa, S. L., Anton, B. P., Kneller, D. W., Petralia, L. M. C., Ganatra, M. B., Boisvert, M. L., Vainauskas, S., Chan, S.-H., Hokke, C. H., Foster, J. M., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105437 · Cited by 7

Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison

Guo, Z., Wang, Y., & Ou, G. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae064 · Cited by 6

Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis

Blackwell, A. M., Jami-Alahmadi, Y., Nasamu, A. S., Kudo, S., Senoo, A., Slam, C., Tsumoto, K., Wohlschlegel, J. A., Manuel Martinez Caaveiro, J., Goldberg, D. E., et al. (2024) · eLife · doi:10.7554/elife.100256 · Cited by 5

Structural basis for human chondroitin sulfate chain polymerization

(2025) · doi:10.1038/s41467-025-66787-5 · Cited by 5

Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis

(2024) · doi:10.7554/elife.100256.3 · Cited by 5

Novel gurmarin-like peptides from Gymnema sylvestre and their interactions with the sweet taste receptor T1R2/T1R3

(2024) · doi:10.1093/chemse/bjae018 · Cited by 4

Structure of AcMNPV nucleocapsid reveals DNA portal organization and packaging apparatus of circular dsDNA baculovirus

Effantin, G., Kandiah, E., & Pelosse, M. (2025) · Nature Communications · doi:10.1038/s41467-025-60152-2 · Cited by 4

The PCI domains are “winged” HEAT domains

Paul, E. E., & Marintchev, A. (2022) · PLOS ONE · doi:10.1371/journal.pone.0268664 · Cited by 4

Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing

Breidenstein, A., ter Beek, J., & Berntsson, R. P.-A. (2023) · Life Science Alliance · doi:10.26508/lsa.202201775 · Cited by 3

Genomic and culture-based analysis of Cyclaneusma minus in New Zealand provides evidence for multiple morphotypes

Tarallo, M., Dobbie, K. B., Leite, L. N., Waters, T. L., Gillard, K. N. T., Sen, D., Mesarich, C. H., Bradshaw, R. E., & McDougal, R. L. (2024) · Phytopathology Research · doi:10.1186/s42483-024-00255-8 · Cited by 3

Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse

Elofsson, A., Han, L., Bianchi, E., Wright, G. J., & Jovine, L. (2023) · doi:10.1101/2023.07.27.550195 · Cited by 3

Crystal Structure of Bifidobacterium bifidum Glycoside Hydrolase Family 110 α-Galactosidase Specific for Blood Group B Antigen

(2024) · doi:10.5458/jag.jag.jag-2024_0005 · Cited by 2

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) · doi:10.1101/2024.07.16.603793 · Cited by 1

The SSU Processome Component Utp25p is a Pseudohelicase

Helwer, R., & Charette, J. M. (2022) · doi:10.1101/2022.07.08.499361 · Cited by 1

Intraflagellar transport protein IFT172 contains a C-terminal ubiquitin-binding U-box-like domain involved in ciliary signaling

Zacharia, N. K., Kuhns, S., Boegholm, N., Christensen, A., Wang, J., Petriman, N. A., Lorentzen, A., Fialova, J. L., Menguy, L., Saunier, S., et al. (2026) · eLife · doi:10.7554/elife.104906.3 · Cited by 1

Intraflagellar transport protein IFT172 contains a C-terminal ubiquitin-binding U-box-like domain involved in ciliary signaling

Zacharia, N. K., Kuhns, S., Boegholm, N., Christensen, A., Wang, J., Petriman, N. A., Lorentzen, A., Fialova, J. L., Menguy, L., Saunier, S., et al. (2026) · eLife · doi:10.7554/elife.104906