The Buccaneer software for automated model building. 1. Tracing protein chains

Features and development of Coot

Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915

Overview of the CCP 4 suite and current developments

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353

Crystal structure of Cas9 in complex with guide RNA and target DNA

Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

Langer, G., Cohen, S. X., Lamzin, V. S., & Perrakis, A. (2008) · Nature Protocols · doi:10.1038/nprot.2008.91 · Cited by 1,606

Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen

Pallesen, J., Wang, N., Corbett, K. S., Wrapp, D., Kirchdoerfer, R. N., Turner, H. L., Cottrell, C. A., Becker, M. M., Wang, L., Shi, W., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1707304114 · Cited by 1,073

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0848-2 · Cited by 888

Retroviral intasome assembly and inhibition of DNA strand transfer

Hare, S., Gupta, S. S., Valkov, E., Engelman, A., & Cherepanov, P. (2010) · Nature · doi:10.1038/nature08784 · Cited by 678

Non-Homeostatic Body Weight Regulation Through a Brainstem-Restricted Receptor for GDF15

Hsu, J.-Y., Crawley, S., Chen, M., Ayupova, D. A., Lindhout, D. A., Higbee, J., Kutach, A., Joo, W., Gao, Z., Fu, D., et al. (2017) · Nature · doi:10.1038/nature24042 · Cited by 616

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Walls, A. C., Xiong, X., Park, Y.-J., Tortorici, M. A., Snijder, J., Quispe, J., Cameroni, E., Gopal, R., Dai, M., Lanzavecchia, A., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.028 · Cited by 582

Structure and control of the actin regulatory WAVE complex

Chen, Z., Borek, D., Padrick, S. B., Gomez, T. S., Metlagel, Z., Ismail, A. M., Umetani, J., Billadeau, D. D., Otwinowski, Z., & Rosen, M. K. (2010) · Nature · doi:10.1038/nature09623 · Cited by 500

Structure of the membrane domain of respiratory complex I

Efremov, R. G., & Sazanov, L. A. (2011) · Nature · doi:10.1038/nature10330 · Cited by 370

Structural insights into HDAC6 tubulin deacetylation and its selective inhibition

Miyake, Y., Keusch, J. J., Wang, L., Saito, M., Hess, D., Wang, X., Melancon, B. J., Helquist, P., Gut, H., & Matthias, P. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2140 · Cited by 315

Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases

Canning, P., Cooper, C. D. O., Krojer, T., Murray, J. W., Pike, A. C. W., Chaikuad, A., Keates, T., Thangaratnarajah, C., Hojzan, V., Marsden, B. D., et al. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.437996 · Cited by 284

A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

Fletcher, J. M., Boyle, A. L., Bruning, M., Bartlett, G. J., Vincent, T. L., Zaccai, N. R., Armstrong, C. T., Bromley, E. H. C., Booth, P. J., Brady, R. L., et al. (2012) · ACS Synthetic Biology · doi:10.1021/sb300028q · Cited by 262

Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense

Wiedenheft, B., Zhou, K., Jinek, M., Coyle, S. M., Ma, W., & Doudna, J. A. (2009) · Structure · doi:10.1016/j.str.2009.03.019 · Cited by 229

Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.

Laverty, D., Thomas, P., Field, M., Andersen, O. J., Gold, M. G., Biggin, P. C., Gielen, M., & Smart, T. G. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3477 · Cited by 179

Protein sequence design with a learned potential

Anand, N., Eguchi, R., Mathews, I. I., Perez, C. P., Derry, A., Altman, R. B., & Huang, P.-S. (2022) · Nature Communications · doi:10.1038/s41467-022-28313-9 · Cited by 171

Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

Tailford, L. E., Owen, C. D., Walshaw, J., Crost, E. H., Hardy-Goddard, J., Le Gall, G., de Vos, W. M., Taylor, G. L., & Juge, N. (2015) · Nature Communications · doi:10.1038/ncomms8624 · Cited by 183

Structural basis and regulation of the reductive stress response

Manford, A. G., Mena, E. L., Shih, K. Y., Gee, C. L., McMinimy, R., Martínez-González, B., Sherriff, R., Lew, B., Zoltek, M., Rodríguez-Pérez, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.002 · Cited by 152

Crystal structure of the human lysosomal mTORC1 scaffold complex and its impact on signaling

de Araujo, M. E. G., Naschberger, A., Fürnrohr, B. G., Stasyk, T., Dunzendorfer-Matt, T., Lechner, S., Welti, S., Kremser, L., Shivalingaiah, G., Offterdinger, M., et al. (2017) · Science · doi:10.1126/science.aao1583 · Cited by 134

Mechanistic insights into neurotransmitter release and presynaptic plasticity from the crystal structure of Munc13-1 C1C2BMUN

Xu, J., Camacho, M., Xu, Y., Esser, V., Liu, X., Trimbuch, T., Pan, Y.-Z., Ma, C., Tomchick, D. R., Rosenmund, C., et al. (2017) · eLife · doi:10.7554/elife.22567 · Cited by 119

Repulsive guidance molecule is a structural bridge between neogenin and bone morphogenetic protein

Healey, E. G., Bishop, B., Elegheert, J., Bell, C. H., Padilla-Parra, S., & Siebold, C. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3016 · Cited by 112

Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice

Guo, S., Stevens, C. A., Vance, T. D. R., Olijve, L. L. C., Graham, L. A., Campbell, R. L., Yazdi, S. R., Escobedo, C., Bar-Dolev, M., Yashunsky, V., et al. (2017) · Science Advances · doi:10.1126/sciadv.1701440 · Cited by 107

Ribosomal oxygenases are structurally conserved from prokaryotes to humans

Chowdhury, R., Sekirnik, R., Brissett, N. C., Krojer, T., Ho, C.-H., Ng, S. S., Clifton, I. J., Ge, W., Kershaw, N. J., Fox, G. C., et al. (2014) · Nature · doi:10.1038/nature13263 · Cited by 105

Structure and function of cohesin's Scc3/SA regulatory subunit

Roig, M. B., Löwe, J., Chan, K.-L., Beckouët, F., Metson, J., & Nasmyth, K. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.08.015 · Cited by 91

The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes

De, I., Bessonov, S., Hofele, R., dos Santos, K., Will, C. L., Urlaub, H., Lührmann, R., & Pena, V. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2951 · Cited by 89

Recognition of protein-linked glycans as a determinant of peptidase activity

Noach, I., Ficko-Blean, E., Pluvinage, B., Stuart, C., Jenkins, M. L., Brochu, D., Buenbrazo, N., Wakarchuk, W., Burke, J. E., Gilbert, M., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1615141114 · Cited by 89

Structure of the Ca2+-dependent PP2A heterotrimer and insights into Cdc6 dephosphorylation

Wlodarchak, N., Guo, F., Satyshur, K. A., Jiang, L., Jeffrey, P. D., Sun, T., Stanevich, V., Mumby, M. C., & Xing, Y. (2013) · Cell Research · doi:10.1038/cr.2013.77 · Cited by 72

Progressive assembly of multi-domain protein structures from cryo-EM density maps

Zhou, X., Li, Y., Zhang, C., Zheng, W., Zhang, G., & Zhang, Y. (2022) · Nature Computational Science · doi:10.1038/s43588-022-00232-1 · Cited by 75

Structural basis of protein phosphatase 2A stable latency

Jiang, L., Stanevich, V., Satyshur, K. A., Kong, M., Watkins, G. R., Wadzinski, B. E., Sengupta, R., & Xing, Y. (2013) · Nature Communications · doi:10.1038/ncomms2663 · Cited by 68

Structure of the bacterial cell division determinant GpsB and its interaction with penicillin‐binding proteins

Rismondo, J., Cleverley, R. M., Lane, H. V., Großhennig, S., Steglich, A., Möller, L., Mannala, G. K., Hain, T., Lewis, R. J., & Halbedel, S. (2016) · Molecular Microbiology · doi:10.1111/mmi.13279 · Cited by 55

ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat

Nishio, S., Emori, C., Wiseman, B., Fahrenkamp, D., Dioguardi, E., Zamora-Caballero, S., Bokhove, M., Han, L., Stsiapanava, A., Algarra, B., et al. (2024) · Cell · doi:10.1016/j.cell.2024.02.013 · Cited by 54

Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold

Castells-Graells, R., Meador, K., Arbing, M. A., Sawaya, M. R., Gee, M., Cascio, D., Gleave, E., Debreczeni, J. É., Breed, J., Leopold, K., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2305494120 · Cited by 48

piRNA processing by a trimeric Schlafen-domain nuclease

Podvalnaya, N., Bronkhorst, A. W., Lichtenberger, R., Hellmann, S., Nischwitz, E., Falk, T., Karaulanov, E., Butter, F., Falk, S., & Ketting, R. F. (2023) · Nature · doi:10.1038/s41586-023-06588-2 · Cited by 47

Structure and function of virion RNA polymerase of a crAss-like phage

Drobysheva, A. V., Panafidina, S. A., Kolesnik, M. V., Klimuk, E. I., Minakhin, L., Yakunina, M. V., Borukhov, S., Nilsson, E., Holmfeldt, K., Yutin, N., et al. (2021) · Nature · doi:10.1038/s41586-020-2921-5 · Cited by 44

The Human Mixed Lineage Leukemia 5 (MLL5), a Sequentially and Structurally Divergent SET Domain-Containing Protein with No Intrinsic Catalytic Activity

Mas-y-Mas, S., Barbon, M., Teyssier, C., Déméné, H., Carvalho, J. E., Bird, L. E., Lebedev, A., Fattori, J., Schubert, M., Dumas, C., et al. (2016) · PLOS ONE · doi:10.1371/journal.pone.0165139 · Cited by 43

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.

Vance, T. D. R., Olijve, L. L. C., Campbell, R. L., Voets, I. K., Davies, P. L., & Guo, S. (2014) · Bioscience Reports · doi:10.1042/bsr20140083 · Cited by 40

Molecular replacement: tricks and treats

Abergel, C. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913015291 · Cited by 36

CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae

Weaver, S. J., Ortega, D. R., Sazinsky, M. H., Dalia, T. N., Dalia, A. B., & Jensen, G. J. (2020) · Nature Communications · doi:10.1038/s41467-020-18866-y · Cited by 37

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

Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif

Siponen, M. I., Wisniewska, M., Lehtiö, L., Johansson, I., Svensson, L., Raszewski, G., Nilsson, L., Sigvardsson, M., & Berglund, H. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.c110.150482 · Cited by 34

Structural and functional analysis of EntV reveals a 12 amino acid fragment protective against fungal infections

Cruz, M. R., Cristy, S., Guha, S., De Cesare, G. B., Evdokimova, E., Sanchez, H., Borek, D., Miramón, P., Yano, J., Fidel, P. L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33613-1 · Cited by 30

Structural analysis of haemoglobin binding by HpuA from the Neisseriaceae family

Wong, C. T., Xu, Y., Gupta, A., Garnett, J. A., Matthews, S. J., & Hare, S. A. (2015) · Nature Communications · doi:10.1038/ncomms10172 · Cited by 30

Comparative Structural and Thermal Stability Studies of Cuc m 2.0101, Art v 4.0101 and Other Allergenic Profilins

Kapingidza, A. B., Pye, S. E., Hyduke, N., Dolamore, C., Pote, S., Schlachter, C. R., Commins, S. P., Kowal, K., & Chruszcz, M. (2019) · Molecular Immunology · doi:10.1016/j.molimm.2019.07.004 · Cited by 30

DNA-bridging by an archaeal histone variant via a unique tetramerisation interface

(2023) · doi:10.1038/s42003-023-05348-2 · Cited by 25

MrParse : finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more

Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322003576 · Cited by 24

Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction

(2022) · doi:10.1093/nar/gkac563 · Cited by 22

Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara

(2023) · doi:10.1186/s13068-023-02307-1 · Cited by 16

An unbroken network of interactions connecting flagellin domains is required for motility in viscous environments

Nedeljković, M., Kreutzberger, M. A. B., Postel, S., Bonsor, D., Xing, Y., Jacob, N., Schuler, W. J., Egelman, E. H., & Sundberg, E. J. (2023) · PLOS Pathogens · doi:10.1371/journal.ppat.1010979 · Cited by 13

Kinetoplastid kinetochore proteins KKT14–KKT15 are divergent Bub1/BubR1–Bub3 proteins

Ballmer, D., Carter, W., van Hooff, J. J. E., Tromer, E. C., Ishii, M., Ludzia, P., & Akiyoshi, B. (2024) · Open Biology · doi:10.1098/rsob.240025 · Cited by 13

Structural and functional analyses of viral H2 protein of the vaccinia virus entry fusion complex

Kao, C.-F., Liu, C.-Y., Hsieh, C.-L., Carillo, K. J. D., Tzou, D.-L. M., Wang, H.-C., & Chang, W. (2023) · Journal of Virology · doi:10.1128/jvi.01343-23 · Cited by 12

The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells

Fernández, I., Dynesen, L. T., Coquin, Y., Pederzoli, R., Brun, D., Haouz, A., Gessain, A., Rey, F. A., Buseyne, F., & Backovic, M. (2023) · Nature Communications · doi:10.1038/s41467-023-36923-0 · Cited by 11

Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Fraser, A., Sokolova, M. L., Drobysheva, A. V., Gordeeva, J. V., Borukhov, S., Jumper, J., Severinov, K. V., & Leiman, P. G. (2022) · Nature Communications · doi:10.1038/s41467-022-31214-6 · Cited by 7

Determinants of receptor tyrosine phosphatase homophilic adhesion: Structural comparison of PTPRK and PTPRM extracellular domains

Hay, I. M., Shamin, M., Caroe, E. R., Mohammed, A. S. A., Svergun, D. I., Jeffries, C. M., Graham, S. C., Sharpe, H. J., & Deane, J. E. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102750 · Cited by 7

The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail

Ludzia, P., Ishii, M., Deák, G., Spanos, C., Wilson, M. D., Redfield, C., & Akiyoshi, B. (2025) · Structure · doi:10.1016/j.str.2024.10.031 · Cited by 6

The complete λ-carrageenan depolymerization cascade from a marine Pseudoalteromonad revealed by structural analysis of the enzymes

Vickers, C. J., Hettle, A. G., Hobbs, J. K., Shapiro-Ward, S., Pluvinage, B., Medley, B. J., McGuire, B. E., Mihalynuk, L., Nitin, N., Zandberg, W. F., et al. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.110719 · Cited by 6

Divergent polo boxes in KKT2 bind KKT1 to initiate the kinetochore assembly cascade in Trypanosoma brucei

Ishii, M., Ludzia, P., Marcianò, G., Allen, W., Nerusheva, O. O., & Akiyoshi, B. (2022) · Molecular Biology of the Cell · doi:10.1091/mbc.e22-07-0269-t · Cited by 5

Molecular structure of the ESCRT-III-based archaeal CdvAB cell division machinery

Drobnič, T., Salzer, R., Nierhaus, T., Jiang, M. K. X., Bellini, D., Steindorf, A., Albers, S.-V., Baum, B., & Löwe, J. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2525941123 · Cited by 5

piRNA processing by a trimeric Schlafen-domain nuclease

Podvalnaya, N., Bronkhorst, A. W., Lichtenberger, R., Hellmann, S., Nischwitz, E., Falk, T., Karaulanov, E., Butter, F., Falk, S., & Ketting, R. F. (2023) · doi:10.1101/2023.01.19.524756 · 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

Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara

Junghare, M., Manavalan, T., Fredriksen, L., Leiros, I., Altermark, B., Eijsink, V. G. H., & Vaaje-Kolstad, G. (2023) · doi:10.21203/rs.3.rs-2475918/v1 · Cited by 2

Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean

Krull, J., Sidhu, C., Solanki, V., Bligh, M., Rößler, L., Singh, R. K., Huang, G., Robb, C. S., Teeling, H., Seeberger, P. H., et al. (2026) · Microbiome · doi:10.1186/s40168-026-02379-9 · Cited by 2

HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold

(2024) · doi:10.1002/prot.26673 · Cited by 1

Determinants of receptor tyrosine phosphatase homophilic adhesion: structural comparison of PTPRK and PTPRM extracellular domains

(2022) · doi:10.1101/2022.06.23.497309 · Cited by 1

Molecular mechanism and structural models of protein-mediated copper transfer to the Arabidopsis thaliana ethylene receptor ETR1 at the ER membrane

(2025) · doi:10.1038/s41598-025-19915-6 · Cited by 1

Molecular Mechanism and Structural Models of Protein-Mediated Copper Transfer to the Arabidopsis thaliana Ethylene Receptor ETR1 at the ER Membrane

Dluhosch, D., Kersten, L. S., Minges, A., Schott-Verdugo, S., Gohlke, H., & Groth, G. (2025) · doi:10.1101/2025.01.21.634023