Addendum: Accurate structure prediction of biomolecular interactions with AlphaFold 3

Citations

Cited by:

1. Samantha F. Sedor & Sichen Shao, 2025. "Mechanism of ASF1 engagement by CDAN1," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
2. Ai Tamura & Kazuyuki Yamagata & Takashi Kono & Masanori Fujimoto & Takahiro Fuchigami & Motoi Nishimura & Masataka Yokoyama & Akitoshi Nakayama & Naoko Hashimoto & Ikki Sakuma & Nobuyuki Mitsukawa & Y, 2025. "p53-inducible lncRNA LOC644656 causes genotoxic stress-induced stem cell maldifferentiation and cancer chemoresistance," Nature Communications, Nature, vol. 16(1), pages 1-22, December.
3. 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.
4. Pantelis Livanos & Choy Kriechbaum & Sophia Remers & Arvid Herrmann & Sabine Müller, 2025. "Kinesin-12 POK2 polarization is a prerequisite for a fully functional division site and aids cell plate positioning," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
5. 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.
6. 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.
7. Elisa Posani & Pavel Janoš & Daniel Haack & Navtej Toor & Massimiliano Bonomi & Alessandra Magistrato & Giovanni Bussi, 2025. "Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
8. 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.
9. Chuwen Zhang & Yong He & Jieni Wang & Tengkai Chen & Federico Baltar & Minjie Hu & Jing Liao & Xi Xiao & Zhao-Rong Li & Xiyang Dong, 2025. "LucaPCycle: Illuminating microbial phosphorus cycling in deep-sea cold seep sediments using protein language models," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
10. F. Li & A. S. Phadte & M. Bhatia & S. Barndt & A. R. Monte Carlo III & C-F. D. Hou & R. Yang & S. Strock & A. Pluciennik, 2025. "Structural and molecular basis of PCNA-activated FAN1 nuclease function in DNA repair," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
11. 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.
12. Sisira Mambram Kunnath & Elad Arad & Ran Zalk & Itamar Kass & Anat Shahar & Albert Batushansky & Hanna Rapaport & Raz Jelinek, 2025. "Allosteric amyloid catalysis by coiled coil fibrils," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
13. 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.
14. 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.
15. 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.
16. 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.
17. Jinhao Que & Guangfu Xue & Tao Wang & Xiyun Jin & Zuxiang Wang & Yideng Cai & Wenyi Yang & Meng Luo & Qian Ding & Jinwei Zhang & Yilin Wang & Yuexin Yang & Fenglan Pang & Yi Hui & Zheng Wei & Jun Xion, 2025. "Identifying T cell antigen at the atomic level with graph convolutional network," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
18. 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.
19. Qingshan Luo & Chengai Wang & Shuai Qiao & Shan Yu & Lianwan Chen & Seonghoon Kim & Kun Wang & Jiangge Zheng & Yong Zhang & Fan Wu & Xiaoguang Lei & Jizhong Lou & Michael Hennig & Wonpil Im & Long Mia, 2025. "Surface lipoprotein sorting by crosstalk between Lpt and Lol pathways in gram-negative bacteria," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
20. 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.
21. Florian Malard & Kristen Dias & Margaux Baudy & Stéphane Thore & Brune Vialet & Philippe Barthélémy & Sébastien Fribourg & Fedor V. Karginov & Sébastien Campagne, 2025. "Molecular basis for the calcium-dependent activation of the ribonuclease EndoU," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
22. Tim C. Hewitt & Keshav Sharma & Jianping Zhang & Chunhong Chen & Prabin Bajgain & Dhara Bhatt & Smriti Singh & Pablo D. Olivera Firpo & Jun Yang & Qiaoli Wang & Narayana Upadhyaya & Curtis Pozniak & R, 2025. "Divergent molecular pathways govern temperature-dependent wheat stem rust resistance genes," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
23. 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.
24. 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.
25. Ji Huang & Liang Tong, 2025. "Molecular insights into the overall architecture of human rixosome," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
26. 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.
27. 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.
28. Stephen A. Rettie & Katelyn V. Campbell & Asim K. Bera & Alex Kang & Simon Kozlov & Yensi Flores Bueso & Joshmyn Cruz & Maggie Ahlrichs & Suna Cheng & Stacey R. Gerben & Mila Lamb & Analisa Murray & V, 2025. "Cyclic peptide structure prediction and design using AlphaFold2," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
29. Luciano A. Masullo & Rafal Kowalewski & Monique Honsa & Larissa Heinze & Shuhan Xu & Philipp R. Steen & Heinrich Grabmayr & Isabelle Pachmayr & Susanne C. M. Reinhardt & Ana Perovic & Jisoo Kwon & Eth, 2025. "Spatial and stoichiometric in situ analysis of biomolecular oligomerization at single-protein resolution," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
30. 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.
31. 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.
32. Tanmoy Paul & Chunli Yan & Jina Yu & Susan E. Tsutakawa & John A. Tainer & Dong Wang & Ivaylo Ivanov, 2025. "Molecular model of TFIIH recruitment to the transcription-coupled repair machinery," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
33. Julien Herrou & Laetitia My & Caroline L. Monteil & Marine Bergot & Rikesh Jain & Emmanuelle Martinez & Tâm Mignot, 2025. "Tad pili with adaptable tips mediate contact-dependent killing during bacterial predation," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
34. Jane Dudley-Fraser & Diego Esposito & Katherine A. McPhie & Coltrane Morley-Williams & Tania Auchynnikava & Katrin Rittinger, 2025. "Identification of RING E3 pseudoligases in the TRIM protein family," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
35. Tianyang Zhao & Kuipei Jin & Xiaodong Wang & Xiong Su & Youjun Wang & Mingming Gao & Wen Luo & Hongyuan Yang & Zhongzhou Yang, 2025. "GPAT4 sustains endoplasmic reticulum homeostasis in endocardial cells and safeguards heart development," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
36. Qi Gao & Florian W. Hofer & Sebastian Filbeck & Bram J. A. Vermeulen & Martin Würtz & Annett Neuner & Charlotte Kaplan & Maja Zezlina & Cornelia Sala & Hyesu Shin & Oliver J. Gruss & Elmar Schiebel & , 2025. "Structural mechanisms for centrosomal recruitment and organization of the microtubule nucleator γ-TuRC," Nature Communications, Nature, vol. 16(1), pages 1-23, December.
37. Jinsheng Fan & Renzhi Li & Mingmeng Zhao & Xishan Pan, 2025. "A BiLSTM-Based Hybrid Ensemble Approach for Forecasting Suspended Sediment Concentrations: Application to the Upper Yellow River," Land, MDPI, vol. 14(6), pages 1-29, June.
38. Savannah J. Weeks-Pollenz & Matthew J. Petrides & Kaylie A. Padgett-Pagliai & Robert Davis & Kathryn K. Harris & Linda B. Bloom, 2025. "The YoaA-χ helicase modulates the dynamics of single-stranded DNA binding protein on DNA," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
39. Julian O. Streit & Sammy H. S. Chan & Saifu Daya & John Christodoulou, 2025. "Rational design of 19F NMR labelling sites to probe protein structure and interactions," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
40. 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.
41. 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.
42. Petersen, Alexander Michael & Arroyave, Felber J. & Pammolli, Fabio, 2025. "The disruption index suffers from citation inflation: Re-analysis of temporal CD trend and relationship with team size reveal discrepancies," Journal of Informetrics, Elsevier, vol. 19(1).
43. 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.
44. 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.
45. Melissa V. Gammons & Elsa Franco-Echevarría & Tie-Mei Li & Trevor J. Rutherford & Miha Renko & Christopher Batters & Mariann Bienz, 2025. "Wnt signalosome assembly is governed by conformational flexibility of Axin and by the AP2 clathrin adaptor," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
46. Joel T. Rämö & Bryan R. Gorman & Lu-Chen Weng & Sean J. Jurgens & Panisa Singhanetr & Marisa G. Tieger & Elon HC Dijk & Christopher W. Halladay & Xin Wang & Blake M. Hauser & Soo Hyun Kim & Joost Brin, 2025. "Rare genetic variation in PTPRB is associated with central serous chorioretinopathy, varicose veins and glaucoma," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
47. Matthew D. Mann & Min Wang & Josephine C. Ferreon & Phoebe S. Tsoi & Michael P. Suess & Antrix Jain & Anna Malovannaya & Roberto Vera Alvarez & Bruce D. Pascal & Raj Kumar & Dean P. Edwards & Patrick , 2025. "Structural proteomics defines a sequential priming mechanism for the progesterone receptor," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
48. Brittany Cain & Zhenyu Yuan & Evelyn Thoman & Rhett A. Kovall & Brian Gebelein, 2025. "The ALX4 dimer structure provides insight into how disease alleles impact function," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
49. Xinwei Song & Yiling Wang & Youjing Wang & Kankan Zhao & Di Tong & Ruichuan Gao & Xiaofei Lv & Dedong Kong & Yunjie Ruan & Mengcen Wang & Xianjin Tang & Fangbai Li & Yongming Luo & Yongguan Zhu & Jian, 2025. "Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
50. 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.
51. 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.
52. 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.
53. 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.
54. Eliott S. Wenger & David W. Christianson, 2025. "Structure of bifunctional variediene synthase yields unique insight on biosynthetic diterpene assembly and cyclization," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
55. John R. Horton & Meigen Yu & Jujun Zhou & Melody Tran & Rithvi R. Anakal & Yue Lu & Robert M. Blumenthal & Xiaotian Zhang & Yun Huang & Xing Zhang & Xiaodong Cheng, 2025. "Multimeric transcription factor BCL11A utilizes two zinc-finger tandem arrays to bind clustered short sequence motifs," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
56. Michal Beffinger & Linda Schellhammer & Betül Taskoparan & Sereina Deplazes & Ulisse Salazar & Nazanin Tatari & Frauke Seehusen & Leopold Balthazar & Carl Philipp Zinner & Sabine Spath & Tala Shekaria, 2025. "FcRn-silencing of IL-12Fc prevents toxicity of local IL-12 therapy and prolongs survival in experimental glioblastoma," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
57. Lena Peters & Moritz Drechsler & Michael A. Herrera & Jing Liu & Barbara Pees & Johanna Jarstorff & Anna Czerwinski & Francesca Lubbock & Georgia Angelidou & Liesa Salzer & Karlis Arturs Moors & Nicol, 2025. "Polyketide synthase-derived sphingolipids mediate microbiota protection against a bacterial pathogen in C. elegans," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
58. Xiaofei Jiao & Zhongyang Liang & Jiwei Li & Long Bai & Jun Xu & Yidan Liu & Lin-Yu Lu, 2025. "Aberrant activation of chromosome asynapsis checkpoint triggers oocyte elimination," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
59. Yu Wang & Sen Wang & Yuanyuan Chen & Chunlan Xie & Haibo Xu & Yunhua Lin & Ranxun Lin & Wanlin Zeng & Xuan Chen & Xinyi Nie & Shihua Wang, 2025. "The role of Npt1 in regulating antifungal protein activity in filamentous fungi," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
60. Chaoming Wang & Sichao He & Shouwei Luo & Yuxiang Huan & Si Wu, 2025. "Integrating physical units into high-performance AI-driven scientific computing," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
61. 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.
62. 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.