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Highly accurate protein structure prediction with AlphaFold

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Kazuki Kato & Sae Okazaki & Soumya Kannan & Han Altae-Tran & F. Esra Demircioglu & Yukari Isayama & Junichiro Ishikawa & Masahiro Fukuda & Rhiannon K. Macrae & Tomohiro Nishizawa & Kira S. Makarova & , 2022. "Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
Xiansha Xiao & Allison Fay & Pablo Santos Molina & Amanda Kovach & Michael S. Glickman & Huilin Li, 2024. "Structure of the M. tuberculosis DnaK−GrpE complex reveals how key DnaK roles are controlled," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
Ye Yuan & Lei Chen & Kexu Song & Miaomiao Cheng & Ling Fang & Lingfei Kong & Lanlan Yu & Ruonan Wang & Zhendong Fu & Minmin Sun & Qian Wang & Chengjun Cui & Haojue Wang & Jiuyang He & Xiaonan Wang & Y, 2024. "Stable peptide-assembled nanozyme mimicking dual antifungal actions," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
Lisa T. Pulianmackal & Jose Miguel I. Limcaoco & Keerthikka Ravi & Sinyu Yang & Jeffrey Zhang & Mimi K. Tran & Maria Ghalmi & Matthew J. O’Meara & Anthony G. Vecchiarelli, 2023. "Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
Wei Lu & Jixian Zhang & Weifeng Huang & Ziqiao Zhang & Xiangyu Jia & Zhenyu Wang & Leilei Shi & Chengtao Li & Peter G. Wolynes & Shuangjia Zheng, 2024. "DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
Marcos Gil-Garcia & Ana I. Benítez-Mateos & Marcell Papp & Florence Stoffel & Chiara Morelli & Karl Normak & Katarzyna Makasewicz & Lenka Faltova & Francesca Paradisi & Paolo Arosio, 2024. "Local environment in biomolecular condensates modulates enzymatic activity across length scales," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
Nabin Giri & Jianlin Cheng, 2024. "De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
Yutaka Maruyama & Ayori Mitsutake, 2022. "Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach," J, MDPI, vol. 5(1), pages 1-12, February.
Aleksandra Levina & Kaelin D. Fleming & John E. Burke & Thomas A. Leonard, 2022. "Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
Bin Xue & Zoobia Bashir & Yachong Guo & Wenting Yu & Wenxu Sun & Yiran Li & Yiyang Zhang & Meng Qin & Wei Wang & Yi Cao, 2023. "Strong, tough, rapid-recovery, and fatigue-resistant hydrogels made of picot peptide fibres," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
Pengdbamba Dieudonné Zongo & Nicolas Cabanel & Guilhem Royer & Florence Depardieu & Alain Hartmann & Thierry Naas & Philippe Glaser & Isabelle Rosinski-Chupin, 2024. "An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
Vinitha N. Ragavan & Pramod C. Nair & Natalia Jarzebska & Ramcharan Singh Angom & Luana Ruta & Elisa Bianconi & Silvia Grottelli & Natalia D. Tararova & Daniel Ryazanskiy & Steven R. Lentz & Sara Tomm, 2023. "A multicentric consortium study demonstrates that dimethylarginine dimethylaminohydrolase 2 is not a dimethylarginine dimethylaminohydrolase," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
Ivica Odorčić & Mohamed Belal Hamed & Sam Lismont & Lucía Chávez-Gutiérrez & Rouslan G. Efremov, 2024. "Apo and Aβ46-bound γ-secretase structures provide insights into amyloid-β processing by the APH-1B isoform," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
Zhengrui Zhang & Jiaqi Fu & Johannes Gregor Matthias Rack & Chuang Li & Jim Voorneveld & Dmitri V. Filippov & Ivan Ahel & Zhao-Qing Luo & Chittaranjan Das, 2024. "Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
Agnes Adler & Mamata Bangera & J. Wouter Beugelink & Salima Bahri & Hugo Ingen & Carolyn A. Moores & Marc Baldus, 2024. "A structural and dynamic visualization of the interaction between MAP7 and microtubules," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
Jeremy R. Keown & Adam D. Crawshaw & Jose Trincao & Loïc Carrique & Richard J. Gildea & Sam Horrell & Anna J. Warren & Danny Axford & Robin Owen & Gwyndaf Evans & Annie Bézier & Peter Metcalf & Jonath, 2023. "Atomic structure of a nudivirus occlusion body protein determined from a 70-year-old crystal sample," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
Yiqi Jiang & Zhijiao Sun & Kexin Lu & Zeyu Wu & Hailong Xue & Li Zhu & Guosi Li & Yun Feng & Mianbin Wu & Jianping Lin & Jiazhang Lian & Lirong Yang, 2023. "Manipulation of sterol homeostasis for the production of 24-epi-ergosterol in industrial yeast," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
Kohdai Yamada & Ryouhei Shioya & Kohei Nishino & Hirotake Furihata & Atsushi Hijikata & Mika K. Kaneko & Yukinari Kato & Tsuyoshi Shirai & Hidetaka Kosako & Tatsuya Sawasaki, 2023. "Proximity extracellular protein-protein interaction analysis of EGFR using AirID-conjugated fragment of antigen binding," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
Léon Faure & Bastien Mollet & Wolfram Liebermeister & Jean-Loup Faulon, 2023. "A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
Zhao Yang & Xue Zhang & Shiwei Ye & Jingtao Zheng & Xiaowei Huang & Fang Yu & Zhenguo Chen & Shiqing Cai & Peng Zhang, 2023. "Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
Deike J. Omnus & Matthias J. Fink & Aswathy Kallazhi & Maria Xandri Zaragoza & Axel Leppert & Michael Landreh & Kristina Jonas, 2023. "The heat shock protein LarA activates the Lon protease in response to proteotoxic stress," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
Louis Tung Faat Lai & Jayashree Balaraman & Fei Zhou & Doreen Matthies, 2023. "Cryo-EM structures of human magnesium channel MRS2 reveal gating and regulatory mechanisms," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
Tian Zhu & Merry H. Ma, 2022. "Deriving the Optimal Strategy for the Two Dice Pig Game via Reinforcement Learning," Stats, MDPI, vol. 5(3), pages 1-14, August.
Yuze Sun & Xuyao Liu & Wenmao Huang & Shimin Le & Jie Yan, 2024. "Structural domain in the Titin N2B-us region binds to FHL2 in a force-activation dependent manner," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
Lanlan Cai & Hang Liu & Wen Zhang & Shiwei Xiao & Qinglu Zeng & Shangyu Dang, 2023. "Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
Ngat T. Tran & Tung B. K. Le, 2024. "Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
Rezwan Siddiquee & Carol H. Pong & Ruth M. Hall & Sandro F. Ataide, 2024. "A programmable seekRNA guides target selection by IS1111 and IS110 type insertion sequences," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
Lasse M. Blaabjerg & Nicolas Jonsson & Wouter Boomsma & Amelie Stein & Kresten Lindorff-Larsen, 2024. "SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
Maryna V. Ivanchenko & Daniel M. Hathaway & Alex J. Klein & Bifeng Pan & Olga Strelkova & Pedro De-la-Torre & Xudong Wu & Cole W. Peters & Eric M. Mulhall & Kevin T. Booth & Corey Goldstein & Joseph B, 2023. "Mini-PCDH15 gene therapy rescues hearing in a mouse model of Usher syndrome type 1F," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
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.
Ryan P. Hildebrandt & Kathryn R. Moss & Aleksandra Janusz-Kaminska & Luke A. Knudson & Lance T. Denes & Tanvi Saxena & Devi Prasad Boggupalli & Zhuangyue Li & Kun Lin & Gary J. Bassell & Eric T. Wang, 2023. "Muscleblind-like proteins use modular domains to localize RNAs by riding kinesins and docking to membranes," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
Vasista Adupa & Elizaveta Ustyantseva & Harm H. Kampinga & Patrick R. Onck, 2024. "Tertiary structure and conformational dynamics of the anti-amyloidogenic chaperone DNAJB6b at atomistic resolution," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
Jienyu Ding & Yun-Tzai Lee & Yuba Bhandari & Charles D. Schwieters & Lixin Fan & Ping Yu & Sergey G. Tarosov & Jason R. Stagno & Buyong Ma & Ruth Nussinov & Alan Rein & Jinwei Zhang & Yun-Xing Wang, 2023. "Visualizing RNA conformational and architectural heterogeneity in solution," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
Xintao Yan & Zhengxia Zou & Shuo Feng & Haojie Zhu & Haowei Sun & Henry X. Liu, 2023. "Learning naturalistic driving environment with statistical realism," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
Alessandro Boverio & Neelam Jamil & Barbara Mannucci & Maria Laura Mascotti & Marco W. Fraaije & Andrea Mattevi, 2024. "Structure, mechanism, and evolution of the last step in vitamin C biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
Nikos Pinotsis & Anna Krüger & Nicolas Tomas & Spyros D. Chatziefthymiou & Claudia Litz & Simon Arnold Mortensen & Mamadou Daffé & Hedia Marrakchi & Garabed Antranikian & Matthias Wilmanns, 2023. "Discovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
Shao-Yang Li & Gao-Qian Wang & Liang Long & Jia-Ling Gao & Zheng-Qun Zhou & Yong-Heng Wang & Jian-Ming Lv & Guo-Dong Chen & Dan Hu & Ikuro Abe & Hao Gao, 2024. "Functional and structural dissection of glycosyltransferases underlying the glycodiversity of wolfberry-derived bioactive ingredients lycibarbarspermidines," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
Jingying Zhang & Grigory Maksaev & Peng Yuan, 2023. "Open structure and gating of the Arabidopsis mechanosensitive ion channel MSL10," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
Yuvaraj Bhoobalan-Chitty & Shuanshuan Xu & Laura Martinez-Alvarez & Svetlana Karamycheva & Kira S. Makarova & Eugene V. Koonin & Xu Peng, 2024. "Regulatory sequence-based discovery of anti-defense genes in archaeal viruses," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
Duanfang Cao & Bingting Ma & Ziyi Cao & Xiaoyu Xu & Xinzheng Zhang & Ye Xiang, 2024. "The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
Zhong Li & Lilan Zhang & Kangwei Xu & Yuanyuan Jiang & Jieke Du & Xingwang Zhang & Ling-Hong Meng & Qile Wu & Lei Du & Xiaoju Li & Yuechan Hu & Zhenzhen Xie & Xukai Jiang & Ya-Jie Tang & Ruibo Wu & Re, 2023. "Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
Stella Vitt & Simone Prinz & Martin Eisinger & Ulrich Ermler & Wolfgang Buckel, 2022. "Purification and structural characterization of the Na+-translocating ferredoxin: NAD+ reductase (Rnf) complex of Clostridium tetanomorphum," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
Pierre Azoulay & Joshua Krieger & Abhishek Nagaraj, 2024. "Old Moats for New Models: Openness, Control, and Competition in Generative AI," NBER Chapters, in: Entrepreneurship and Innovation Policy and the Economy, volume 4, National Bureau of Economic Research, Inc.
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Pok Man Leung & Rhys Grinter & Eve Tudor-Matthew & James P. Lingford & Luis Jimenez & Han-Chung Lee & Michael Milton & Iresha Hanchapola & Erwin Tanuwidjaya & Ashleigh Kropp & Hanna A. Peach & Carlo R, 2024. "Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
Riya Shah & Thomas C. Panagiotou & Gregory B. Cole & Trevor F. Moraes & Brigitte D. Lavoie & Christopher A. McCulloch & Andrew Wilde, 2024. "The DIAPH3 linker specifies a β-actin network that maintains RhoA and Myosin-II at the cytokinetic furrow," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
Joka Pipercevic & Bastian Kohl & Ruta Gerasimaite & Véronique Comte-Miserez & Sarah Hostachy & Thomas Müntener & Elia Agustoni & Henning Jacob Jessen & Dorothea Fiedler & Andreas Mayer & Sebastian Hil, 2023. "Inositol pyrophosphates activate the vacuolar transport chaperone complex in yeast by disrupting a homotypic SPX domain interaction," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
Yashan Yang & Qianqian Shao & Mingcheng Guo & Lin Han & Xinyue Zhao & Aohan Wang & Xiangyun Li & Bo Wang & Ji-An Pan & Zhenguo Chen & Andrei Fokine & Lei Sun & Qianglin Fang, 2024. "Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
Anthony C. Bishop & Glorisé Torres-Montalvo & Sravya Kotaru & Kyle Mimun & A. Joshua Wand, 2023. "Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
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Wanyue Xu & Yue Yu & Juli Jing & Zhen Wu & Xumin Zhang & Chenjiang You & Hong Ma & Gregory P. Copenhaver & Yan He & Yingxiang Wang, 2023. "SCFRMF mediates degradation of the meiosis-specific recombinase DMC1," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
Juan Manuel Valverde & Geronimo Dubra & Michael Phillips & Austin Haider & Carlos Elena-Real & Aurélie Fournet & Emile Alghoul & Dhanvantri Chahar & Nuria Andrés-Sanchez & Matteo Paloni & Pau Bernadó , 2023. "A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
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Dinesh Gupta & Keying Chen & Sean J. Elliott & Dipti D. Nayak, 2024. "MmcA is an electron conduit that facilitates both intracellular and extracellular electron transport in Methanosarcina acetivorans," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
Patrick Bryant & Atharva Kelkar & Andrea Guljas & Cecilia Clementi & Frank Noé, 2024. "Structure prediction of protein-ligand complexes from sequence information with Umol," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
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James H. Thierer & Ombretta Foresti & Pradeep Kumar Yadav & Meredith H. Wilson & Tabea O. C. Moll & Meng-Chieh Shen & Elisabeth M. Busch-Nentwich & Margaret Morash & Karen L. Mohlke & John F. Rawls & , 2024. "Pla2g12b drives expansion of triglyceride-rich lipoproteins," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
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Yanan Zhao & Jiaojiao Hu & Shan-Shan Yang & Jing Zhong & Jianping Liu & Shuo Wang & Yuzhuo Jiao & Fang Jiang & Ruiyang Zhai & Bingnan Ren & Hua Cong & Yuwei Zhu & Fengtong Han & Jixian Zhang & Yue Xu , 2022. "A redox switch regulates the assembly and anti-CRISPR activity of AcrIIC1," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
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Jun-Yu Si & Yuan-Mei Chen & Ye-Hui Sun & Meng-Xue Gu & Mei-Ling Huang & Lu-Lu Shi & Xiao Yu & Xiao Yang & Qing Xiong & Cheng-Bao Ma & Peng Liu & Zheng-Li Shi & Huan Yan, 2024. "Sarbecovirus RBD indels and specific residues dictating multi-species ACE2 adaptiveness," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
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John C. K. Wang & Hannah T. Baddock & Amirhossein Mafi & Ian T. Foe & Matthew Bratkowski & Ting-Yu Lin & Zena D. Jensvold & Magdalena Preciado López & David Stokoe & Dan Eaton & Qi Hao & Aaron H. Nile, 2024. "Structure of the p53 degradation complex from HPV16," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
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Josie L. Ferreira & Vojtěch Pražák & Daven Vasishtan & Marc Siggel & Franziska Hentzschel & Annika M. Binder & Emma Pietsch & Jan Kosinski & Friedrich Frischknecht & Tim W. Gilberger & Kay Grünewald, 2023. "Variable microtubule architecture in the malaria parasite," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
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Xiaodi Yu & Rosalie E. Matico & Robyn Miller & Dhruv Chauhan & Bertrand Schoubroeck & Karolien Grauwen & Javier Suarez & Beth Pietrak & Nandan Haloi & Yanting Yin & Gary John Tresadern & Laura Perez-B, 2024. "Structural basis for the oligomerization-facilitated NLRP3 activation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
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Matthew C. Metcalf & Benjamin M. Janus & Rui Yin & Ruixue Wang & Johnathan D. Guest & Edwin Pozharski & Mansun Law & Roy A. Mariuzza & Eric A. Toth & Brian G. Pierce & Thomas R. Fuerst & Gilad Ofek, 2023. "Structure of engineered hepatitis C virus E1E2 ectodomain in complex with neutralizing antibodies," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
Deyun Qiu & Jinxin V. Pei & James E. O. Rosling & Vandana Thathy & Dongdi Li & Yi Xue & John D. Tanner & Jocelyn Sietsma Penington & Yi Tong Vincent Aw & Jessica Yi Han Aw & Guoyue Xu & Abhai K. Tripa, 2022. "A G358S mutation in the Plasmodium falciparum Na+ pump PfATP4 confers clinically-relevant resistance to cipargamin," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
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Shuo-Shuo Liu & Tian-Xia Jiang & Fan Bu & Ji-Lan Zhao & Guang-Fei Wang & Guo-Heng Yang & Jie-Yan Kong & Yun-Fan Qie & Pei Wen & Li-Bin Fan & Ning-Ning Li & Ning Gao & Xiao-Bo Qiu, 2024. "Molecular mechanisms underlying the BIRC6-mediated regulation of apoptosis and autophagy," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
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R. Čepaitė & N. Klein & A. Mikšys & S. Camara-Wilpert & V. Ragožius & F. Benz & A. Skorupskaitė & H. Becker & G. Žvejytė & N. Steube & G.K.A Hochberg & L. Randau & R. Pinilla-Redondo & L. Malinauskait, 2024. "Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
Thibault R. Bongiovanni & Casey J. Latario & Youn Cras & Evan Trus & Sophie Robitaille & Kerry Swartz & Danica Schmidtke & Maxence Vincent & Artemis Kosta & Jan Orth & Florian Stengel & Riccardo Pella, 2024. "Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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