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Accurate structure prediction of biomolecular interactions with AlphaFold 3

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  1. Samantha F. Sedor & Sichen Shao, 2025. "Mechanism of ASF1 engagement by CDAN1," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  2. Ho Yee Joyce Fung & Sanraj R. Mittal & Ashley B. Niesman & Jenny Jiou & Binita Shakya & Takuya Yoshizawa & Ahmet E. Cansizoglu & Michael P. Rout & Yuh Min Chook, 2025. "Phosphate-dependent nuclear export via a non-classical NES class recognized by exportin Msn5," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  3. Yanyi Song & Shuyi Jian & Junlin Teng & Pengli Zheng & Zhe Zhang, 2025. "Structural basis of human VANGL-PRICKLE interaction," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  4. Cornelia Sala & Martin Würtz & Enrico Salvatore Atorino & Annett Neuner & Patrick Partscht & Thomas Hoffmann & Sebastian Eustermann & Elmar Schiebel, 2024. "An interaction network of inner centriole proteins organised by POC1A-POC1B heterodimer crosslinks ensures centriolar integrity," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  5. Jake Colautti & Huagang Tan & Nathan P. Bullen & Stephanie S. Thang & Dirk Hackenberger & Andrew C. Doxey & John C. Whitney, 2024. "A widespread accessory protein family diversifies the effector repertoire of the type VI secretion system spike," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  6. Sanghyeon Choi & Youngjin Lee & Shinhye Park & Song Yee Jang & Jongbin Park & Do Won Oh & Su-Man Kim & Tae-Hwan Kim & Ga Seul Lee & Changyi Cho & Byoung Sik Kim & Donghan Lee & Eun-Hee Kim & Hae-Kap C, 2024. "Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  7. Gašper Šolinc & Marija Srnko & Franci Merzel & Ana Crnković & Mirijam Kozorog & Marjetka Podobnik & Gregor Anderluh, 2025. "Cryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipids," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  8. Heng Zhou & Xiaoling He & Yue Xiong & Yixuan Gong & Yuanyuan Zhang & Shuangli Li & Rui Hu & Ying Li & Xu Zhang & Xin Zhou & Jiang Zhu & Yunhuang Yang & Maili Liu, 2025. "Structural insights into a highly flexible zinc finger module unravel INSM1 function in transcription regulation," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  9. Xibing Xu & Roland Barriot & Bertille Voisin & Tom J. Arrowsmith & Ben Usher & Claude Gutierrez & Xue Han & Carine Pagès & Peter Redder & Tim R. Blower & Olivier Neyrolles & Pierre Genevaux, 2024. "Nucleotidyltransferase toxin MenT extends aminoacyl acceptor ends of serine tRNAs to control Mycobacterium tuberculosis growth," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  10. Timothy K. Soh & Sofia Ognibene & Saskia Sanders & Robin Schäper & Benedikt B. Kaufer & Jens B. Bosse, 2024. "A proteome-wide structural systems approach reveals insights into protein families of all human herpesviruses," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  11. Juan M. Perez-Bertoldi & Yuanchang Zhao & Akanksha Thawani & Ahmet Yildiz & Eva Nogales, 2024. "HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  12. Xin Yong & Guowen Jia & Qin Yang & Chunzhuang Zhou & Sitao Zhang & Huaqing Deng & Daniel D. Billadeau & Zhaoming Su & Da Jia, 2025. "Cryo-EM structure of the BLOC-3 complex provides insights into the pathogenesis of Hermansky-Pudlak syndrome," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  13. Yinghui Chen & Yunxin Xu & Di Liu & Yaoguang Xing & Haipeng Gong, 2024. "An end-to-end framework for the prediction of protein structure and fitness from single sequence," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  14. Na Jiang & Hekun Yang & Yi Lei & Weida Qin & Huifang Xiong & Kuan Chen & Kunrong Mei & Gongyu Li & Xin Mu & Ruibing Chen, 2025. "Characterization of dsRNA binding proteins through solubility analysis identifies ZNF385A as a dsRNA homeostasis regulator," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
  15. Jieyi Li & Simiao Gong & Yuan Ma & Peiyan Han & Nan Wang & Zongheng Fu & Xinyi Zhang & Xinyang Huang & Tianyu Yang & Hanze Tong & Guang-Rong Zhao & Yi Wu & Ying-Jin Yuan, 2025. "Creation of a eukaryotic multiplexed site-specific inversion system and its application for metabolic engineering," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  16. Bing Wang & Nelly Said & Tarek Hilal & Mark Finazzo & Markus C. Wahl & Irina Artsimovitch, 2025. "Nucleotide-induced hyper-oligomerization inactivates transcription termination factor ρ," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  17. Jiaxin Tan & Yuan Xiao & Fang Kong & Jiawei Qian & Angqi Zhu & Chuangye Yan, 2025. "Structural insights into thyroid hormone transporter MCT8," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
  18. Lavanya Manjunath & Gisselle Santiago & Pedro Ortega & Ambrocio Sanchez & Sunwoo Oh & Alexander Garcia & Junyi Li & Dana Duong & Elodie Bournique & Alexis Bouin & Bert L. Semler & Dheva Setiaputra & R, 2025. "Cooperative role of PACT and ADAR1 in preventing aberrant PKR activation by self-derived double-stranded RNA," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  19. Tongqing Li & Steven E. Stayrook & Wenxue Li & Yueyue Wang & Hengyi Li & Jianan Zhang & Yansheng Liu & Daryl E. Klein, 2025. "Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  20. Michael Kugler & Felix J. Metzner & Gregor Witte & Karl-Peter Hopfner & Katja Lammens, 2024. "Phosphorylation-mediated conformational change regulates human SLFN11," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  21. Mingxin Guo & Qun Lian & Ye Mei & Wangwang Yang & Suna Zhao & Siyuan Zhang & Xinfeng Xing & Haixiang Zhang & Keying Gao & Wentong He & Zhitong Wang & Huan Wang & Jun Zhou & Lin Cheng & Zhigui Bao & Sa, 2024. "Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  22. Fernanda A. Sala & Katja Ditter & Olexandr Dybkov & Henning Urlaub & Hauke S. Hillen, 2025. "Structural basis of Nipah virus RNA synthesis," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  23. Lucas A. Defelipe & Katharina Veith & Osvaldo Burastero & Tatiana Kupriianova & Isabel Bento & Michal Skruzny & Knut Kölbel & Charlotte Uetrecht & Roland Thuenauer & Maria M. García-Alai, 2024. "Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  24. Tae-Kyeong Jeong & R. Ciaran MacKenzie Frater & Jongha Yoon & Anja Groth & Ji-Joon Song, 2025. "CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  25. Maxime Zamba-Campero & Daniel Soliman & Huaxin Yu & Amanda G. Lasseter & Yuen-Yan Chang & Julia L. Silberman & Jun Liu & L. Aravind & Mollie W. Jewett & Gisela Storz & Philip P. Adams, 2024. "Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  26. Timothy Atkinson & Thomas D. Barrett & Scott Cameron & Bora Guloglu & Matthew Greenig & Charlie B. Tan & Louis Robinson & Alex Graves & Liviu Copoiu & Alexandre Laterre, 2025. "Protein sequence modelling with Bayesian flow networks," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  27. Reilly Pidgeon & Sacha Mitchell & Michael Shamash & Layan Suleiman & Lharbi Dridi & Corinne F. Maurice & Bastien Castagner, 2025. "Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
  28. Marina Chiara Garassino & Kunle Odunsi & Marciano Siniscalchi & Pietro Veronesi, 2025. "On the Economic Infeasibility of Personalized Medicine, and a Solution," NBER Working Papers 33539, National Bureau of Economic Research, Inc.
  29. Xuhang Lu & Dongmei Li & Yaojie Wang & Gaohua Zhang & Tianlei Wen & Yue Lu & Nan Jia & Xuedi Wang & Shenghai Chang & Xing Zhang & Jianping Lin & Yu-hang Chen & Xue Yang & Yuequan Shen, 2025. "Structural insights into the activation mechanism of the human zinc-activated channel," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  30. Yannick Weyer & Sinead I. Schwabl & Xuechen Tang & Astha Purwar & Konstantin Siegmann & Angela Ruepp & Theresia Dunzendorfer-Matt & Michael A. Widerin & Veronika Niedrist & Noa J. M. Mutsters & Maria , 2024. "The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  31. Christoph Humberg & Zahide Yilmaz & Katharina Fitzian & Wolfgang Dörner & Daniel Kümmel & Henning D. Mootz, 2025. "A cysteine-less and ultra-fast split intein rationally engineered from being aggregation-prone to highly efficient in protein trans-splicing," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  32. Ruifang Ma & Bowen Du & Chen Shi & Lei Wang & Fuxing Zeng & Jie Han & Huiyi Guan & Yong Wang & Kaige Yan, 2025. "Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca2+," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  33. Kehan Wu & Yingce Xia & Pan Deng & Renhe Liu & Yuan Zhang & Han Guo & Yumeng Cui & Qizhi Pei & Lijun Wu & Shufang Xie & Si Chen & Xi Lu & Song Hu & Jinzhi Wu & Chi-Kin Chan & Shawn Chen & Liangliang Z, 2024. "TamGen: drug design with target-aware molecule generation through a chemical language model," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  34. Meili Li & Chengming Zhu & Zheng Xu & Mingjing Xu & Yan Kuang & Xinhao Hou & Xinya Huang & Mengqi Lv & Yongrui Liu & Yong Zhang & Ziyan Xu & Xu Han & Suman Wang & Yunyu Shi & Shouhong Guang & Fudong L, 2024. "Structural basis for C. elegans pairing center DNA binding specificity by the ZIM/HIM-8 family proteins," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  35. Yue Peng & Junze Wu & Yi Sun & Yuanxing Zhang & Qiyao Wang & Shuai Shao, 2025. "Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
  36. Fabian Ries & Jasmin Gorlt & Sabrina Kaiser & Vanessa Scherer & Charlotte Seydel & Sandra Nguyen & Andreas Klingl & Julia Legen & Christian Schmitz-Linneweber & Hinrik Plaggenborg & Jediael Z. Y. Ng &, 2025. "A truncated variant of the ribosome-associated trigger factor specifically contributes to plant chloroplast ribosome biogenesis," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  37. Jiawei Ge & Ting Wang & Hongwei Yu & Lidan Ye, 2025. "De novo biosynthesis of nylon 12 monomer ω-aminododecanoic acid," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  38. Wenkai Chen & Xueying Xu & Zhidan Zeng & Mingsen Zhou & Jiying Chen & Guangfu Hu & Anfu Shen & Dapeng Li & Liu Xiangjiang, 2025. "The role of pyruvate dehydrogenase in the lifespan determination of daphnids," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  39. Haaris A. Safdari & Martino Morici & Ana Sanchez-Castro & Andrea Dallapè & Helge Paternoga & Anna Maria Giuliodori & Attilio Fabbretti & Pohl Milón & Daniel N. Wilson, 2025. "The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  40. Luc Provencher & Wilson Nartey & Peter M. Brownlee & Austin W. Atkins & Jean-Philippe Gagné & Lou Baudrier & Nicholas S. Y. Ting & Cortt G. Piett & Shujuan Fang & Dustin D. Pearson & Shaun Moore & Pie, 2025. "CHD6 has poly(ADP-ribose)- and DNA-binding domains and regulates PARP1/2-trapping inhibitor sensitivity via abasic site repair," Nature Communications, Nature, vol. 16(1), pages 1-24, December.
  41. Nathalie Béchon & Nitzan Tal & Avigail Stokar-Avihail & Alon Savidor & Meital Kupervaser & Sarah Melamed & Gil Amitai & Rotem Sorek, 2024. "Diversification of molecular pattern recognition in bacterial NLR-like proteins," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  42. Ji Huang & Liang Tong, 2025. "Molecular insights into the overall architecture of human rixosome," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  43. Sophia Vincoff & Shrey Goel & Kseniia Kholina & Rishab Pulugurta & Pranay Vure & Pranam Chatterjee, 2025. "FusOn-pLM: a fusion oncoprotein-specific language model via adjusted rate masking," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  44. Yida Jiang & Xinghe Zhang & Honggang Nie & Jianxiong Fan & Shuangshuang Di & Hui Fu & Xiu Zhang & Lijuan Wang & Chun Tang, 2024. "Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  45. Ian Y. Yen & Gregory B. Whitfield & John L. Rubinstein & Lori L. Burrows & Yves V. Brun & P. Lynne Howell, 2025. "Conformational changes in the motor ATPase CpaF facilitate a rotary mechanism of Tad pilus assembly," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
  46. Yijia Cheng & Mark A. B. Kreutzberger & Jianting Han & Edward H. Egelman & Qin Cao, 2024. "Molecular architecture of the assembly of Bacillus spore coat protein GerQ revealed by cryo-EM," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  47. Juan G. Carvajal-Patiño & Vincent Mallet & David Becerra & Luis Fernando Niño Vasquez & Carlos Oliver & Jérôme Waldispühl, 2025. "RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  48. Fan Zhang & Shaobai Li & Hao Wu & Shanshuang Chen, 2025. "Cryo-EM structure and oligomerization of the human planar cell polarity core protein Vangl1," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  49. Z. Faidon Brotzakis & Shengyu Zhang & Mhd Hussein Murtada & Michele Vendruscolo, 2025. "AlphaFold prediction of structural ensembles of disordered proteins," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
  50. Jianan Zhang & Yuko Tsutsui & Hengyi Li & Tongqing Li & Yueyue Wang & Salma Laraki & Sofia Alarcon-Frias & Steven E. Stayrook & Daryl E. Klein, 2025. "Structural basis for the interaction between the Drosophila RTK Sevenless (dROS1) and the GPCR BOSS," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  51. James Hodgkinson-Bean & Rafael Ayala & Nadishka Jayawardena & Georgia L. Rutter & Bridget N. J. Watson & David Mayo-Muñoz & James Keal & Peter C. Fineran & Matthias Wolf & Mihnea Bostina, 2025. "Global structural survey of the flagellotropic myophage φTE infecting agricultural pathogen Pectobacterium atrosepticum," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  52. Jason Saba & Katia Flores & Bailey Marshall & Michael D. Engstrom & Yikai Peng & Atharv S. Garje & Laurie E. Comstock & Robert Landick, 2024. "Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
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  62. Théophile Niault & Ariel Talavera & Eric Le Cam & Sonia Baconnais & Ole Skovgaard & Florian Fournes & Léa Wagner & Hedvig Tamman & Andrew Thompson & Dannele Echemendia-Blanco & Noa Guzzi & Abel Garcia, 2025. "Dynamic transitions of initiator binding coordinate the replication of the two chromosomes in Vibrio cholerae," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
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  78. William J. Nicolas & Anna Shiriaeva & Michael W. Martynowycz & Angus C. Grey & Yasmeen N. Ruma & Paul J. Donaldson & Tamir Gonen, 2025. "Structure of the lens MP20 mediated adhesive junction," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
  79. Wen Yang & Man Feng & Kuohai Yu & Jie Cao & Guangxian Cui & Yumei Zhang & Huiru Peng & Yingyin Yao & Zhaorong Hu & Zhongfu Ni & Feng Qin & Fuminori Takahashi & Qixin Sun & Mingming Xin, 2025. "The TaCLE24b peptide signaling cascade modulates lateral root development and drought tolerance in wheat," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
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