ColabFold - Making protein folding accessible to all

UniProt: a worldwide hub of protein knowledge

The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698

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

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005659 · Cited by 2,748

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & the UniProt Consortium (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu739 · Cited by 1,928

HH-suite3 for fast remote homology detection and deep protein annotation

Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., & Söding, J. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3019-7 · Cited by 1,145

Clustering huge protein sequence sets in linear time

Steinegger, M., & Söding, J. (2018) · Nature Communications · doi:10.1038/s41467-018-04964-5 · Cited by 875

MMseqs2 desktop and local web server app for fast, interactive sequence searches

Mirdita, M., Steinegger, M., & Söding, J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty1057 · Cited by 618

MGnify: the microbiome analysis resource in 2020

Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1035 · Cited by 562

Protein complex prediction with AlphaFold-Multimer

Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808

Scientific discovery in the age of artificial intelligence.

Wang, H., Fu, T., Du, Y., Gao, W., Huang, K., Liu, Z., Chandak, P., Liu, S., Van Katwyk, P., Deac, A., et al. (2023) · Nature · doi:10.1038/s41586-023-06221-2 · Cited by 1,823

Harnessing protein folding neural networks for peptide–protein docking

Tsaban, T., Varga, J. K., Avraham, O., Ben-Aharon, Z., Khramushin, A., & Schueler-Furman, O. (2022) · Nature Communications · doi:10.1038/s41467-021-27838-9 · Cited by 1,205

Automated model building and protein identification in cryo-EM maps

Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2023) · doi:10.1101/2023.05.16.541002 · Cited by 686

Automated model building and protein identification in cryo-EM maps

Jamali, K., Käll, L., Zhang, R., Brown, A., Kimanius, D., & Scheres, S. H. W. (2024) · Nature · doi:10.1038/s41586-024-07215-4 · Cited by 686

Clustering predicted structures at the scale of the known protein universe

Barrio-Hernandez, I., Yeo, J., Jänes, J., Mirdita, M., Gilchrist, C. L. M., Wein, T., Varadi, M., Velankar, S., Beltrao, P., & Steinegger, M. (2023) · Nature · doi:10.1038/s41586-023-06510-w · Cited by 362

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

Tubiana, J., Schneidman-Duhovny, D., & Wolfson, H. J. (2022) · Nature Methods · doi:10.1038/s41592-022-01490-7 · Cited by 274

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2

Stein, R. A., & Mchaourab, H. S. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010483 · Cited by 258

Targeted protein degradation via intramolecular bivalent glues

Hsia, O., Hinterndorfer, M., Cowan, A. D., Iso, K., Ishida, T., Sundaramoorthy, R., Nakasone, M. A., Imrichova, H., Schätz, C., Rukavina, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07089-6 · Cited by 222

Multi‐state modeling of G‐protein coupled receptors at experimental accuracy

Heo, L., & Feig, M. (2022) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26382 · Cited by 215

Phages overcome bacterial immunity via diverse anti-defence proteins

(2023) · doi:10.1038/s41586-023-06869-w · Cited by 138

Structural basis of Gabija anti-phage defence and viral immune evasion

Antine, S. P., Johnson, A. G., Mooney, S. E., Leavitt, A., Mayer, M. L., Yirmiya, E., Amitai, G., Sorek, R., & Kranzusch, P. J. (2024) · Nature · doi:10.1038/s41586-023-06855-2 · Cited by 125

A structural biology community assessment of AlphaFold 2 applications

Akdel, M., Pires, D. E. V., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2021) · doi:10.1101/2021.09.26.461876 · Cited by 122

Identification of trypsin-degrading commensals in the large intestine

Li, Y., Watanabe, E., Kawashima, Y., Plichta, D. R., Wang, Z., Ujike, M., Ang, Q. Y., Wu, R., Furuichi, M., Takeshita, K., et al. (2022) · Nature · doi:10.1038/s41586-022-05181-3 · Cited by 106

De novo protein design by inversion of the AlphaFold structure prediction network

Goverde, C. A., Wolf, B., Khakzad, H., Rosset, S., & Correia, B. E. (2023) · Protein Science · doi:10.1002/pro.4653 · Cited by 103

AlphaFold prediction of structural ensembles of disordered proteins

Brotzakis, Z. F., Zhang, S., Murtada, M. H., & Vendruscolo, M. (2025) · Nature Communications · doi:10.1038/s41467-025-56572-9 · Cited by 99

MINSTED nanoscopy enters the Ångström localization range

Weber, M., von der Emde, H., Leutenegger, M., Gunkel, P., Sambandan, S., Khan, T. A., Keller-Findeisen, J., Cordes, V. C., & Hell, S. W. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01519-4 · Cited by 94

Structural principles of B cell antigen receptor assembly

Dong, Y., Pi, X., Bartels-Burgahn, F., Saltukoglu, D., Liang, Z., Yang, J., Alt, F. W., Reth, M., & Wu, H. (2022) · Nature · doi:10.1038/s41586-022-05412-7 · Cited by 82

Bat genomes illuminate adaptations to viral tolerance and disease resistance

Morales, A. E., Dong, Y., Brown, T., Baid, K., Kontopoulos, D. G., Gonzalez, V., Huang, Z., Ahmed, A.-W., Bhuinya, A., Hilgers, L., et al. (2025) · Nature · doi:10.1038/s41586-024-08471-0 · Cited by 78

Building structural models of a whole mycoplasma cell

Maritan, M., Autin, L., Karr, J., Covert, M. W., Olson, A. J., & Goodsell, D. S. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167351 · Cited by 75

Molecular pathway of mitochondrial preprotein import through the TOM–TIM23 supercomplex

Zhou, X., Yang, Y., Wang, G., Wang, S., Sun, D., Ou, X., Lian, Y., & Li, L. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01103-7 · Cited by 72

Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro

Ghani, U., Desta, I., Jindal, A., Khan, O., Jones, G., Hashemi, N., Kotelnikov, S., Padhorny, D., Vajda, S., & Kozakov, D. (2021) · doi:10.1101/2021.09.07.459290 · Cited by 68

Structure of an endogenous mycobacterial MCE lipid transporter

Chen, J., Fruhauf, A., Fan, C., Ponce, J., Ueberheide, B., Bhabha, G., & Ekiert, D. C. (2023) · Nature · doi:10.1038/s41586-023-06366-0 · Cited by 69

Antiviral signalling by a cyclic nucleotide activated CRISPR protease

Rouillon, C., Schneberger, N., Chi, H., Blumenstock, K., Da Vela, S., Ackermann, K., Moecking, J., Peter, M. F., Boenigk, W., Seifert, R., et al. (2023) · Nature · doi:10.1038/s41586-022-05571-7 · Cited by 66

Non-pathogenic E. coli displaying decoy-resistant IL18 mutein boosts anti-tumor and CAR NK cell responses

Yang, S., Sheffer, M., Kaplan, I. E., Wang, Z., Tarannum, M., Dinh, K., Abdulhamid, Y., Bobilev, E., Shapiro, R., Porter, R., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02418-6 · Cited by 66

AlphaDesign: A de novo protein design framework based on AlphaFold

Jendrusch, M., Korbel, J. O., & Sadiq, S. K. (2021) · doi:10.1101/2021.10.11.463937 · Cited by 65

UM171 glues asymmetric CRL3–HDAC1/2 assembly to degrade CoREST corepressors

Yeo, M. J. R., Zhang, O., Xie, X., Nam, E., Payne, N. C., Gosavi, P. M., Kwok, H. S., Iram, I., Lee, C., Li, J., et al. (2025) · Nature · doi:10.1038/s41586-024-08532-4 · Cited by 58

SNX27–Retromer directly binds ESCPE-1 to transfer cargo proteins during endosomal recycling

Simonetti, B., Guo, Q., Giménez-Andrés, M., Chen, K.-E., Moody, E. R. R., Evans, A. J., Chandra, M., Danson, C. M., Williams, T. A., Collins, B. M., et al. (2022) · PLOS Biology · doi:10.1371/journal.pbio.3001601 · Cited by 55

A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure

(2021) · doi:10.1371/journal.pone.0259871 · Cited by 54

Improved Multimer Prediction using Massive Sampling with AlphaFold in CASP15

Wallner, B. (2023) · doi:10.22541/au.168170986.60158084/v1 · Cited by 53

Improved multimer prediction using massive sampling with AlphaFold in CASP15

Wallner, B. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26562 · Cited by 53

MassiveFold: unveiling AlphaFold’s hidden potential with optimized and parallelized massive sampling

Raouraoua, N., Mirabello, C., Véry, T., Blanchet, C., Wallner, B., Lensink, M. F., & Brysbaert, G. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00714-4 · Cited by 51

Converging mechanism of UM171 and KBTBD4 neomorphic cancer mutations

Xie, X., Zhang, O., Yeo, M. J. R., Lee, C., Tao, R., Harry, S. A., Payne, N. C., Nam, E., Paul, L., Li, Y., et al. (2025) · Nature · doi:10.1038/s41586-024-08533-3 · Cited by 50

Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly

(2024) · doi:10.1038/s41586-024-07616-5 · Cited by 46

Structures and activation mechanism of the Gabija anti-phage system

Li, J., Cheng, R., Wang, Z., Yuan, W., Xiao, J., Zhao, X., Du, X., Xia, S., Wang, L., Zhu, B., et al. (2024) · Nature · doi:10.1038/s41586-024-07270-x · Cited by 46

Identification of Iron-Sulfur (Fe-S) Cluster and Zinc (Zn) Binding Sites Within Proteomes Predicted by DeepMind’s AlphaFold2 Program Dramatically Expands the Metalloproteome

Wehrspan, Z. J., McDonnell, R. T., & Elcock, A. H. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167377 · Cited by 45

Molecular basis of the TRAP complex function in ER protein biogenesis

Jaskolowski, M., Jomaa, A., Gamerdinger, M., Shrestha, S., Leibundgut, M., Deuerling, E., & Ban, N. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-00990-0 · Cited by 43

The structure of apolipoprotein B100 from human low-density lipoprotein

Berndsen, Z. T., & Cassidy, C. K. (2025) · Nature · doi:10.1038/s41586-024-08467-w · Cited by 43

Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex

(2025) · doi:10.1038/s41594-025-01557-x · Cited by 40

A pathogen effector FOLD diversified in symbiotic fungi

Teulet, A., Quan, C., Evangelisti, E., Wanke, A., Yang, W., & Schornack, S. (2023) · New Phytologist · doi:10.1111/nph.18996 · Cited by 40

Sequence clustering confounds AlphaFold2

Schafer, J. W., Lee, M., Chakravarty, D., Thole, J. F., Chen, E. A., & Porter, L. L. (2025) · Nature · doi:10.1038/s41586-024-08267-2 · Cited by 38

The ultra-high affinity transport proteins of ubiquitous marine bacteria

Clifton, B. E., Alcolombri, U., Uechi, G.-I., Jackson, C. J., & Laurino, P. (2024) · Nature · doi:10.1038/s41586-024-07924-w · Cited by 37

A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage

Barrett, J., Naduthodi, M. I. S., Mao, Y., Dégut, C., Musiał, S., Salter, A., Leake, M. C., Plevin, M. J., McCormick, A. J., Blaza, J. N., et al. (2024) · Nature Plants · doi:10.1038/s41477-024-01812-x · Cited by 37

A modular DNA origami nanocompartment for engineering a cell-free, protein unfolding and degradation pathway

Huang, J., Jaekel, A., van den Boom, J., Podlesainski, D., Elnaggar, M., Heuer-Jungemann, A., Kaiser, M., Meyer, H., & Saccà, B. (2024) · Nature Nanotechnology · doi:10.1038/s41565-024-01738-7 · Cited by 35

Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan

Urayama, S.-I., Fukudome, A., Hirai, M., Okumura, T., Nishimura, Y., Takaki, Y., Kurosawa, N., Koonin, E. V., Krupovic, M., & Nunoura, T. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01579-5 · Cited by 34

Using AlphaFold for Rapid and Accurate Fixed Backbone Protein Design

Moffat, L., Greener, J. G., & Jones, D. T. (2021) · doi:10.1101/2021.08.24.457549 · Cited by 33

Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane

Park, S. H., Han, J., Jeong, B.-C., Song, J. H., Jang, S. H., Jeong, H., Kim, B. H., Ko, Y.-G., Park, Z.-Y., Lee, K. E., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01111-7 · Cited by 31

Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold

Shomar, H., Georjon, H., Feng, Y., Olympio, B., Guillaume, M., Tesson, F., Cury, J., Wu, F., & Bernheim, A. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02463-z · Cited by 31

The Vibrio cholerae CBASS phage defence system modulates resistance and killing by antifolate antibiotics

Brenzinger, S., Airoldi, M., Ogunleye, A. J., Jugovic, K., Amstalden, M. K., & Brochado, A. R. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01556-y · Cited by 31

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

Liu, J., Guo, Z., Wu, T., Roy, R. S., Chen, C., & Cheng, J. (2023) · Communications Chemistry · doi:10.1038/s42004-023-00991-6 · Cited by 31

Mechanism of receptor assembly via the pleiotropic adipokine Leptin

Tsirigotaki, A., Dansercoer, A., Verschueren, K. H. G., Marković, I., Pollmann, C., Hafer, M., Felix, J., Birck, C., Van Putte, W., Catteeuw, D., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-00941-9 · Cited by 29

In situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque

(2025) · doi:10.1038/s41564-025-02012-9 · Cited by 28

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

Pratt, O. S., Elliott, L. G., Haon, M., Mesdaghi, S., Price, R. M., Simpkin, A. J., & Rigden, D. J. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.01.016 · Cited by 27

Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets

(2023) · doi:10.1038/s41467-023-41312-8 · Cited by 26

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

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

Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores

Datler, J., Hansen, J. M., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. M. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01201-6 · Cited by 23

PCNA recruits cohesin loader Scc2 to ensure sister chromatid cohesion

Psakhye, I., Kawasumi, R., Abe, T., Hirota, K., & Branzei, D. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01064-x · Cited by 23

Complementing machine learning‐based structure predictions with native mass spectrometry

Allison, T. M., Degiacomi, M. T., Marklund, E. G., Jovine, L., Elofsson, A., Benesch, J. L. P., & Landreh, M. (2022) · Protein Science · doi:10.1002/pro.4333 · Cited by 20

Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein

Du, W., Debski-Antoniak, O., Drabek, D., van Haperen, R., van Dortmondt, M., van der Lee, J., Drulyte, I., van Kuppeveld, F. J. M., Grosveld, F., Hurdiss, D. L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49693-0 · Cited by 19

Selection of a promiscuous minimalist cAMP phosphodiesterase from a library of de novo designed proteins

Schnettler, J. D., Wang, M. S., Gantz, M., Bunzel, H. A., Karas, C., Hollfelder, F., & Hecht, M. H. (2024) · Nature Chemistry · doi:10.1038/s41557-024-01490-4 · Cited by 18

AlphaPulldown – a Python package for protein-protein interaction screens using AlphaFold-Multimer

Yu, D., Chojnowski, G., Rosenthal, M., & Kosinski, J. (2022) · doi:10.1101/2022.08.05.502961 · Cited by 17

Structure of the lens MP20 mediated adhesive junction

Nicolas, W. J., Shiriaeva, A., Martynowycz, M. W., Grey, A. C., Ruma, Y. N., Donaldson, P. J., & Gonen, T. (2025) · Nature Communications · doi:10.1038/s41467-025-57903-6 · Cited by 16

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

PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context

Zhong, G., Zhao, Y., Zhuang, D., Chung, W. K., & Shen, Y. (2025) · Nature Communications · doi:10.1038/s41467-025-62318-4 · Cited by 15

Soft disorder modulates the assembly path of protein complexes

Seoane, B., & Carbone, A. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010713 · Cited by 15

Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes

(2024) · doi:10.1038/s41564-024-01825-4 · Cited by 15

Missense variants causing Wiedemann-Steiner syndrome preferentially occur in the KMT2A-CXXC domain and are accurately classified using AlphaFold2

Reynisdottir, T., Anderson, K. J., Boukas, L., & Bjornsson, H. T. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010278 · Cited by 15

Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment

Malbranke, C., Rostain, W., Depardieu, F., Cocco, S., Monasson, R., & Bikard, D. (2023) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1011621 · Cited by 15

The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection

Vieira, M. F. M., Hernandez, G., Zhong, Q., Arbesú, M., Veloso, T., Gomes, T., Martins, M. L., Monteiro, H., Frazão, C., Frankel, G., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-05856-9 · Cited by 14

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

Mechanism of DNA unwinding by MCM8-9 in complex with HROB

(2024) · doi:10.1038/s41467-024-47936-8 · Cited by 13

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

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Gueto-Tettay, C., Tang, D., Happonen, L., Heusel, M., Khakzad, H., Malmström, J., & Malmström, L. (2023) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010457 · Cited by 12

Mouse radial spoke 3 is a metabolic and regulatory hub in cilia

(2025) · doi:10.1038/s41594-025-01594-6 · Cited by 11

A converged ubiquitin‐proteasome pathway for the degradation of TOC and TOM tail‐anchored receptors

Yang, M., Chen, S., Lim, S., Yang, L., Zhong, J. Y., Chan, K. C., Zhao, Z., Wong, K., Wang, J., & Lim, B. L. (2024) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13645 · Cited by 8

The structure of the Tad pilus alignment complex reveals a periplasmic conduit for pilus extension

Evans, S. L., Peretiazhko, I., Karnani, S. Y., Marmont, L. S., Wheeler, J. H. R., Tseng, B. S., Durham, W. M., Whitney, J. C., & Bergeron, J. R. C. (2025) · Nature Communications · doi:10.1038/s41467-025-62457-8 · Cited by 8

Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)

Gogishvili, D., Illes‐Toth, E., Harris, M. J., Hopley, C., Teunissen, C. E., & Abeln, S. (2024) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26656 · Cited by 8

The Escherichia coli replication initiator DnaA is titrated on the chromosome

Olivi, L., Köstlbacher, S., Ludwig, C., Langendoen, M., Claassens, N. J., Ettema, T. J. G., van der Oost, J., ten Wolde, P. R., Hohlbein, J., & Staals, R. H. J. (2025) · Nature Communications · doi:10.1038/s41467-025-63147-1 · Cited by 7

Regulation of kinesin-2 motility by its β-hairpin motif

Webb, S., Toropova, K., Mukhopadhyay, A. G., Nofal, S. D., & Roberts, A. J. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01630-5 · Cited by 7

Helical ultrastructure of the L-ENA spore aggregation factor of a Bacillus paranthracis foodborne outbreak strain

Sleutel, M., Zegeye, E. D., Llarena, A.-K., Pradhan, B., Fislage, M., O’Sullivan, K., Van Gerven, N., Aspholm, M., & Remaut, H. (2024) · Nature Communications · doi:10.1038/s41467-024-51804-w · Cited by 7

SynDLP is a dynamin-like protein of Synechocystis sp. PCC 6803 with eukaryotic features

Gewehr, L., Junglas, B., Jilly, R., Franz, J., Zhu, W. E., Weidner, T., Bonn, M., Sachse, C., & Schneider, D. (2023) · Nature Communications · doi:10.1038/s41467-023-37746-9 · Cited by 6

Caskin2 is a novel talin- and Abi1-binding protein that promotes cell motility

(2024) · doi:10.1242/jcs.262116 · Cited by 6

Subtype-specific alternative splicing events in breast cancer identified by large-scale data analysis

Deguchi, Y., Kikutake, C., & Suyama, M. (2024) · Scientific Reports · doi:10.1038/s41598-024-65035-y · Cited by 5

Structure and function of the human apoptotic scramblase Xkr4

Chakraborty, S., Feng, Z., Lee, S., Alvarenga, O. E., Panda, A., Zhang, S., Bruni, R., Khelashvili, G., Gupta, K., & Accardi, A. (2025) · Nature Communications · doi:10.1038/s41467-025-62739-1 · Cited by 5

Dimerization of GAS2 mediates crosslinking of microtubules and F-actin

An, J., Imasaki, T., Narita, A., Niwa, S., Sasaki, R., Makino, T., Nitta, R., & Kikkawa, M. (2025) · The EMBO Journal · doi:10.1038/s44318-025-00415-2 · Cited by 5

Guiding discovery of protein sequence-structure-function modeling

(2024) · doi:10.1093/bioinformatics/btae002 · Cited by 4

Pervasive, conserved secondary structure in highly charged protein regions

(2023) · doi:10.1371/journal.pcbi.1011565 · Cited by 4

AlphaCRV: a pipeline for identifying accurate binder topologies in mass-modeling with AlphaFold

Guzmán-Vega, F. J., & Arold, S. T. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae131 · Cited by 4

Short-range translocation by a restriction enzyme motor triggers diffusion along DNA

Göse, M., Magill, E. E., Hughes-Games, A., Shaw, S. J., Diffin, F. M., Rawson, T., Nagy, Z., Seidel, R., & Szczelkun, M. D. (2024) · Nature Chemical Biology · doi:10.1038/s41589-023-01504-1 · Cited by 3

EuDockScore: Euclidean graph neural networks for scoring protein–protein interfaces

McFee, M., Kim, J., & Kim, P. M. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae636 · Cited by 3

Fucose as a nutrient ligand for Dikarya and a building block of early diverging lineages

(2023) · doi:10.1186/s43008-023-00123-8 · Cited by 3

AlphaFold Prediction of Structural Ensembles of Disordered Proteins

Brotzakis, Z. F., Zhang, S., & Vendruscolo, M. (2023) · doi:10.21203/rs.3.rs-2659892/v1 · Cited by 2

Improving the quality of co‐evolution intermolecular contact prediction with DisVis

van Keulen, S. C., & Bonvin, A. M. J. J. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26514 · Cited by 2

The coiled-coil domain of E. coli FtsLB is a structurally detuned element critical for modulating its activation in bacterial cell division

(2021) · doi:10.1101/2021.04.21.440662