ColabFold - Making protein folding accessible to all

Mirdita, Milot, Schütze, Konstantin, Moriwaki, Yoshitaka, Heo, Lim, Ovchinnikov, Sergey, Steinegger, Martin·2021·Nature Methods

Cited by (1,085)

Items 601–700 of 1,085

  1. Highly accurate isoform identification for the human transcriptome
    Sommer, Markus J., Cha, Sooyoung, Varabyou, Ales, Rincon, Natalia, Park, Sukhwan, Minkin, Ilia, Pertea, Mihaela, Steinegger, Martin, Salzberg, Steven L. · 2022
  2. Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
    2025
  3. Reliable protein–protein docking with AlphaFold, Rosetta, and replica exchange
    2025
  4. A pathogen effector <scp>FOLD</scp> diversified in symbiotic fungi
    Teulet, Albin, Quan, Clément, Evangelisti, Edouard, Wanke, Alan, Yang, Weibing, Schornack, Sebastian · 2023 · New Phytologist
  5. A central CRMP complex essential for invasion in Toxoplasma gondii
    Mirko Singer, Kathrin Simon, Ignasi Forné, Markus Meissner · 2023 · PLoS Biology
  6. Insights into the GSDMB-mediated cellular lysis and its targeting by IpaH7.8
    Hang Hubert Yin, Jian Hua Zheng, Qiuqiu He, Xuan Zhang, Xuzichao Li, Yongjian Ma, Xiao Liang, Jiaqi Gao, Benjamin L. Kocsis, Zhuang Li et al. · 2023 · Nature Communications
  7. Klebsiella phage KP34gp57 capsular depolymerase structure and function: from a serendipitous finding to the design of active mini-enzymes against K. pneumoniae
    Barbara Maciejewska, Flavia Squeglia, Agnieszka Łątka, Mario Privitera, Sebastian Olejniczak, Paulina Switala, Alessia Ruggiero, Daniela Marasco, Eliza Kramarska, Zuzanna Drulis‐Kawa et al. · 2023 · mBio
  8. Perilipin 1: a systematic review on its functions on lipid metabolism and atherosclerosis in mice and humans
    Camille Desgrouas, Tabea Thalheim, Mathieu Cérino, Catherine Badens, Nathalie Bonello‐Palot · 2024 · Cardiovascular Research
  9. Programmable RNA base editing with photoactivatable CRISPR-Cas13
    Jeonghye Yu, Jongpil Shin, Jihwan Yu, Jihye Kim, Daseuli Yu, Won Do Heo · 2024 · Nature Communications
  10. High-Performance Genetically Encoded Green Fluorescent Biosensors for Intracellular l -Lactate
    Saaya Hario, Giang N. T. Le, Hikaru Sugimoto, Kei Takahashi, Suguru Nishinami, Hirofumi Toda, Selene Li, Jonathan S. Marvin, Shinya Kuroda, Mikhail A. Drobizhev et al. · 2024 · ACS Central Science
  11. Human paraneoplastic antigen Ma2 (PNMA2) forms icosahedral capsids that can be engineered for mRNA delivery
    Victoria J. Madigan, Yugang Zhang, Rumya S. Raghavan, Max E. Wilkinson, Guilhem Faure, Elena Puccio, Michael Segel, Blake Lash, Rhiannon K. Macrae, Feng Zhang · 2024 · Proceedings of the National Academy of Sciences
  12. RNA-guided RNA silencing by an Asgard archaeal Argonaute
    Carolien Bastiaanssen, Pilar Bobadilla Ugarte, Kijun Kim, Giada Finocchio, Yanlei Feng, Todd A. Anzelon, Stephan Köstlbacher, Daniel Tamarit, Thijs J. G. Ettema, Martin Jínek et al. · 2024 · Nature Communications
  13. An engineered AAV targeting integrin alpha V beta 6 presents improved myotropism across species
    Ai Vu Hong, Laurence Suel, Eva Petat, Auriane Dubois, P. Brun, Nicolas Guerchet, Philippe Veron, Jérôme Poupiot, Isabelle Richard · 2024 · Nature Communications
  14. Intragenic DNA inversions expand bacterial coding capacity
    Rachael B. Chanin, Patrick T. West, Jakob Wirbel, Matthew O Gill, Gabriella Z. M. Green, Ryan M. Park, Nora J. Enright, Arjun M. Miklos, Angela Shang-Mei Hickey, Erin F. Brooks et al. · 2024 · Nature
  15. PARAS: High-Accuracy Machine Learning of Substrate Specificities in Nonribosomal Peptide Synthetases
    Barbara R. Terlouw, Chuan Huang, David Meijer, José D D Cediel-Becerra, Ruolin He, Marlene L. Rothe, Matthew Jenner, Shanshan Zhou, Yu Zhang, Christopher D. Fage et al. · 2026 · JACS Au
  16. Mobile integrons encode phage defense systems
    Kieffer, Nicolas, Hipólito, Alberto, Ortiz-Miravalles, Laura, Blanco, Paula, Delobelle, Thomas, Vizuete, Patricia, Ojeda, Francisco Manuel, Jové, Thomas, Jurenas, Dukas, García-Quintanilla, Meritxell et al. · 2025 · Science
  17. The prototypic crAssphage is a linear phage-plasmid
    Danica T. Schmidtke, Angela Shang-Mei Hickey, Jakob Wirbel, Jordan D. Lin, Ivan Liachko, Gavin J. Sherlock, Ami Siddharth Bhatt · 2025 · Cell Host & Microbe
  18. KH domain proteins: Another family of bacterial RNA matchmakers?
    Mikołaj Olejniczak, Xiaofang Jiang, Maciej M. Basczok, Gisela Storz · 2021 · Molecular Microbiology
  19. Artificial intelligence powers protein-folding predictions
    Michael S. Eisenstein · 2021 · Nature
  20. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation
    Fabian Poetz, Joshua H. Corbo, Yevgen Levdansky, Alexander Spiegelhalter, Doris Lindner, Vera Magg, Svetlana Lebedeva, Jörg Schweiggert, Johanna Schott, Eugene Valkov et al. · 2021 · Nature Communications
  21. Nearest neighbor search on embeddings rapidly identifies distant protein relations
    Konstantin Schütze, Michael Heinzinger, Martin Steinegger, Burkhard Rost · 2022 · Frontiers in Bioinformatics
  22. Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction
    Sumin Lee, Seeun Kim, Gyu Rie Lee, Sohee Kwon, Hyeonuk Woo, Chaok Seok, Hahnbeom Park · 2022 · Computational and Structural Biotechnology Journal
  23. Lipoylation is dependent on the ferredoxin FDX1 and dispensable under hypoxia in human cells
    Pallavi R. Joshi, Shayan Sadre, Xiaoyan A. Guo, Jason G. McCoy, Vamsi Krishna Mootha · 2023 · Journal of Biological Chemistry
  24. The SpoVA membrane complex is required for dipicolinic acid import during sporulation and export during germination
    Yongqiang Gao, Rocío del Carmen Barajas‐Ornelas, Jeremy D. Amon, Fernando H. Ramírez‐Guadiana, Assaf Alon, Kelly P. Brock, Debora S. Marks, Andrew C. Kruse, David Z. Rudner · 2022 · Genes & Development
  25. Prediction of protein assemblies by structure sampling followed by interface‐focused scoring
    Olechnovič, Kliment, Valančauskas, Lukas, Dapkūnas, Justas, Venclovas, Česlovas · 2023 · Proteins: Structure, Function, and Bioinformatics
  26. Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex
    McCafferty, Caitlyn L, Papoulas, Ophelia, Jordan, Mareike A, Hoogerbrugge, Gabriel, Nichols, Candice, Pigino, Gaia, Taylor, David W, Wallingford, John B, Marcotte, Edward M · 2022 · eLife
  27. Structure-guided isoform identification for the human transcriptome
    Sommer, Markus J, Cha, Sooyoung, Varabyou, Ales, Rincon, Natalia, Park, Sukhwan, Minkin, Ilia, Pertea, Mihaela, Steinegger, Martin, Salzberg, Steven L · 2022 · eLife
  28. Structure of the RZZ complex and molecular basis of Spindly‐driven corona assembly at human kinetochores
    2022
  29. Mechanism of human PINK1 activation at the TOM complex in a reconstituted system
    2024
  30. Obtaining protein foldability information from computational models of AlphaFold2 and RoseTTAFold
    Sen Liu, Kan Wu, Cheng Chen · 2022 · Computational and Structural Biotechnology Journal
  31. Potently neutralizing and protective anti-human metapneumovirus antibodies target diverse sites on the fusion glycoprotein
    C. Garrett Rappazzo, Ching-Lin Hsieh, Scott A. Rush, Emma S. Esterman, Teresa Delgado, James C. Geoghegan, Anna Z. Wec, Mrunal Sakharkar, Vicente Más, Jason S. McLellan et al. · 2022 · Immunity
  32. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis
    Lothar Kalmbach, Matthieu Bourdon, Ilya N Belevich, Josip Šafran, Adrien Lemaire, Jung‐ok Heo, Sofía Otero, Bernhard Blob, Jérôme Pelloux, Eija Jokitalo et al. · 2023 · Current Biology
  33. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality
    Jessica A. Buchanan, Nikhil R. Varghese, Caitlin L. Johnston, Margaret Sunde · 2023 · Journal of Molecular Biology
  34. Molecular mechanism of decision-making in glycosaminoglycan biosynthesis
    Douglas Sammon, Anja Krueger, Marta Busse‐Wicher, Rhodri M. L. Morgan, Stuart M. Haslam, Benjamin Schumann, David C. Briggs, Erhard Hohenester · 2023 · Nature Communications
  35. CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits
    J. Romero, Gloria Serrano-Bueno, Carolina Camacho‐Fernández, Mateus Henrique Vicente, María Teresa Gil Ruiz, José R. Pérez‐Castiñeira, Javier Pérez-Hormaeche, Fábio Tebaldi Silveira Nogueira, Federico Valverde · 2024 · The Plant Cell
  36. A chemical probe to modulate human GID4 Pro/N-degron interactions
    Dominic D. G. Owens, Matthew E. R. Maitland, Aliakbar Khalili Yazdi, Xiaosheng Song, Viviane Reber, Martin P. Schwalm, Raquel A. C. Machado, Nicolas Bauer, Xu Wang, Magdalena M. Szewczyk et al. · 2024 · Nature Chemical Biology
  37. Structure‐aware deep learning model for peptide toxicity prediction
    Hossein Ebrahimikondori, Darcy Sutherland, Anat Yanai, Amelia Richter, Ali Salehi, Chenkai Li, Lauren Coombe, Monica Kotkoff, René L. Warren, İnanç Birol · 2024 · Protein Science
  38. Giant polyketide synthase enzymes in the biosynthesis of giant marine polyether toxins
    Fallon, Timothy R., Shende, Vikram V., Wierzbicki, Igor H., Pendleton, Amanda L., Watervoot, Nathan F., Auber, Robert P., Gonzalez, David J., Wisecaver, Jennifer H., Moore, Bradley S. · 2024 · Science
  39. Structural basis for mouse LAG3 interactions with the MHC class II molecule I-Ab
    Qianqian Ming, Daniel Antfolk, David A. Price, Anna Manturova, Elliot Medina, Srishti Singh, Charlotte C. Mason, Timothy H. Tran, Keiran S.M. Smalley, Daisy W. Leung et al. · 2024 · Nature Communications
  40. PilY1 regulates the dynamic architecture of the type IV pilus machine in Pseudomonas aeruginosa
    Shuaiqi Guo, Yunjie Chang, Yves V. Brun, P. Lynne Howell, Lori L. Burrows, Jun Liu · 2024 · Nature Communications
  41. Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation
    Lorenzo Brusini, Nicolas Dos Santos Pacheco, E. Tromer, Dominique Soldati-Favre, M. Brochet · 2022 · Journal of Cell Biology
  42. Protenix-v1: Toward High-Accuracy Open-Source Biomolecular Structure Prediction
    Protenix Team, Yuxuan Zhang, Chengyue Gong, Hanyu Zhang, Wenzhi Ma, Zhenyu Liu, Xinshi Chen, Jiaqi Guan, Lan Wang, Yanping Yang et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  43. Structural Modeling of Nanobodies: A Benchmark of State-of-the-Art Artificial Intelligence Programs
    2023
  44. Sequence clustering confounds AlphaFold2
    Schafer, Joseph W., Lee, Myeongsang, Chakravarty, Devlina, Thole, Joseph F., Chen, Ethan A., Porter, Lauren L. · 2025 · Nature
  45. Maize cytosolic invertase INVAN6 ensures faithful meiotic progression under heat stress
    Wei Huang, Yunfei Li, Yan Du, Lingling Pan, Yumin Huang, Hongbing Liu, Yue Zhao, Yunlu Shi, Yong‐Ling Ruan, Zhaobin Dong et al. · 2022 · New Phytologist
  46. Bacterial peroxidases – Multivalent enzymes that enable the use of hydrogen peroxide for microaerobic and anaerobic proliferation
    Daniela S. Barreiro, Ricardo Oliveira, Sofia R. Pauleta · 2023 · Coordination Chemistry Reviews
  47. Identification and classification of papain-like cysteine proteinases
    Fatih Ozhelvaci, Kamil Steczkiewicz · 2023 · Journal of Biological Chemistry
  48. Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily
    Ivan Koludarov, Tobias Senoner, Timothy Jackson, Daniel Dashevsky, Michael Heinzinger, Steven Douglas Aird, Burkhard Rost · 2023 · Nature Communications
  49. A machine learning strategy for the identification of key in silico descriptors and prediction models for IgG monoclonal antibody developability properties
    Andrew B. Waight, David Příhoda, Rojan Shrestha, Kevin James Metcalf, Marc Andre Bailly, Marco Ancona, Talal Widatalla, Zachary A. Rollins, Alan C. Cheng, Danny A. Bitton et al. · 2023 · mAbs
  50. Bacterial flagella hijack type IV pili proteins to control motility
    Xiaolin Liu, Shoichi Tachiyama, Xiaotian Zhou, Rommel A. Mathias, Sharmin Quazi Bonny, Mohammad Firoz Khan, Yue Xin, Anna Roujeinikova, Jun Liu, Karen M. Ottemann · 2024 · Proceedings of the National Academy of Sciences
  51. NAC guides a ribosomal multienzyme complex for nascent protein processing
    Alfred M. Lentzsch, Denis Yudin, Martin Gamerdinger, Sowmya Chandrasekar, Laurenz Rabl, Alain Scaiola, Elke Deuerling, Nenad Ban, Shu‐ou Shan · 2024 · Nature
  52. Optimising CNT-FET biosensor design through modelling of biomolecular electrostatic gating and its application to β-lactamase detection
    Rebecca E. A. Gwyther, Sébastien Côté, Chang‐Seuk Lee, Haosen Miao, Krithika Ramakrishnan, Matteo Palma, D. Dafydd Jones · 2024 · Nature Communications
  53. Integrating machine learning to advance epitope mapping
    Simranjit Grewal, Nidhi Hegde, Stephanie K. Yanow · 2024 · Frontiers in Immunology
  54. DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states
    Yanqing Liu, Joel A. Hrit, Alison A. Chomiak, Stephanie Stransky, Jordan R. Hoffman, Rochelle L. Tiedemann, Ashley K. Wiseman, Leena S. Kariapper, Bradley M. Dickson, Evan J. Worden et al. · 2024 · Molecular Cell
  55. The Specific Capsule Depolymerase of Phage PMK34 Sensitizes Acinetobacter baumannii to Serum Killing
    Karim Abdelkader, Diana Gutiérrez, Agnieszka Łątka, Dimitri Boeckaerts, Zuzanna Drulis‐Kawa, Bjorn Criel, Hans Gerstmans, Amal Safaan, Ahmed S. Khairalla, Yasser Gaber et al. · 2022 · Antibiotics
  56. Loss-of-function variants in MYCBP2 cause neurobehavioural phenotypes and corpus callosum defects
    Lama AlAbdi, Muriel Desbois, Domnița-Valeria Rusnac, Raashda Ainuddin Sulaiman, Jill Anne Rosenfeld, Seema R. Lalani, David R. Murdock, Lindsay Catherine Burrage, Undiagnosed Diseases Network, Ping Yee Billie Au et al. · 2022 · Brain
  57. Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element
    Ashley M. Kretsch, Mayuresh G. Gadgil, Adam J. DiCaprio, Susanna E. Barrett, Bryce L. Kille, Yuanyuan Si, Lingyang Zhu, Douglas A. Mitchell · 2023 · Biochemistry
  58. Protein interactomes for plant lipid biosynthesis and their biotechnological applications
    Yang Xu, Stacy D. Singer, Guanqun Chen · 2023 · Plant Biotechnology Journal
  59. Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies
    Hanke, Leo, Sheward, Daniel J., Pankow, Alec, Vidakovics, Laura Perez, Karl, Vivien, Kim, Changil, Urgard, Egon, Smith, Natalie L., Astorga-Wells, Juan, Ekström, Simon et al. · 2022 · Science Advances
  60. Unmasking of the von Willebrand A-domain surface adhesin CglB at bacterial focal adhesions mediates myxobacterial gliding motility
    Islam, Salim T., Jolivet, Nicolas Y., Cuzin, Clémence, Belgrave, Akeisha M., My, Laetitia, Fleuchot, Betty, Faure, Laura M., Mahanta, Utkarsha, Kezzo, Ahmad A., Saïdi, Fares et al. · 2023 · Science Advances
  61. Molecular mechanism of plasmid elimination by the DdmDE defense system
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  63. Cross-phyla protein annotation by structural prediction and alignment
    Ruperti, Fabian, Papadopoulos, Nikolaos, Musser, Jacob M., Mirdita, Milot, Steinegger, Martin, Arendt, Detlev · 2023 · Genome Biology
  64. Using AlphaFold Multimer to discover interkingdom protein–protein interactions
    Homma, Felix, Lyu, Joy, van der Hoorn, Renier A. L. · 2024 · The Plant Journal
  65. EDS1 complexes are not required for PRR responses and execute TNL‐ETI from the nucleus in Nicotiana benthamiana
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  66. The metagenome‐derived esterase PET40 is highly promiscuous and hydrolyses polyethylene terephthalate ( PET )
    Hongli Zhang, Robert F. Dierkes, Pablo Pérez-García, Elisa Costanzi, Jonas Dittrich, Pablo A. Cea, Marno Gurschke, Violetta M. Applegate, Kristina Partus, Christel Schmeisser et al. · 2023 · FEBS Journal
  67. Engineered Escherichia coli Whole Cell-Mediated Electro-Biocatalysis for Carbon Dioxide to Formic Acid Conversion
    Hongling Shi, Muran Fu, Shuwei Yuan, Yunfeng Lu, Yang Zhuan, Chao Yue, Lunguang Yao, Chuang Xue, Cun‐Duo Tang · 2024 · ACS Sustainable Chemistry & Engineering
  68. Large Roles of Small Proteins
    Aisha T. Burton, Rilee Zeinert, Gisela Storz · 2024 · Annual Review of Microbiology
  69. Cytochrome P450 Enzyme Design by Constraining the Catalytic Pocket in a Diffusion Model
    Qian Wang, Xiaonan Liu, Hejian Zhang, Huanyu Chu, Chao Shi, Lei Justan Zhang, Pi Liu, Pi Liu, Xiaoxi Zhu, Yuwan Liu et al. · 2024 · Research
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    Thomas E. Wales, Aleksandra Pajak, Alžběta Roeselová, Santosh Shivakumaraswamy, Steven A. Howell, Svend Kjær, F. Ulrich Hartl, John R. Engen, David Balchin · 2024 · Nature Structural & Molecular Biology
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  76. Protein Engineering for Industrial Biocatalysis: Principles, Approaches, and Lessons from Engineered PETases
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  94. The oxidoreductase activity of Rnf balances redox cofactors during fermentation of glucose to propionate in Prevotella
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  98. LDO proteins and Vac8 form a vacuole-lipid droplet contact site to enable starvation-induced lipophagy in yeast
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  99. Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes
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  100. TnpB homologues exapted from transposons are RNA-guided transcription factors
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