Hierarchical graph learning for protein–protein interaction
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-36736-1
Download full text from publisher
References listed on IDEAS
- Klemens Engelberg & Tyler Bechtel & Cynthia Michaud & Eranthie Weerapana & Marc-Jan Gubbels, 2022. "Proteomic characterization of the Toxoplasma gondii cytokinesis machinery portrays an expanded hierarchy of its assembly and function," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
- Charles P. Couturier & Shamini Ayyadhury & Phuong U. Le & Javad Nadaf & Jean Monlong & Gabriele Riva & Redouane Allache & Salma Baig & Xiaohua Yan & Mathieu Bourgey & Changseok Lee & Yu Chang David Wa, 2020. "Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy," Nature Communications, Nature, vol. 11(1), pages 1-1, December.
- Charles P. Couturier & Shamini Ayyadhury & Phuong U. Le & Javad Nadaf & Jean Monlong & Gabriele Riva & Redouane Allache & Salma Baig & Xiaohua Yan & Mathieu Bourgey & Changseok Lee & Yu Chang David Wa, 2020. "Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy," Nature Communications, Nature, vol. 11(1), pages 1-19, December.
- Nicolas Renaud & Cunliang Geng & Sonja Georgievska & Francesco Ambrosetti & Lars Ridder & Dario F. Marzella & Manon F. Réau & Alexandre M. J. J. Bonvin & Li C. Xue, 2021. "DeepRank: a deep learning framework for data mining 3D protein-protein interfaces," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
- Joshua H. Siegle & Xiaoxuan Jia & Séverine Durand & Sam Gale & Corbett Bennett & Nile Graddis & Greggory Heller & Tamina K. Ramirez & Hannah Choi & Jennifer A. Luviano & Peter A. Groblewski & Ruweida , 2021. "Survey of spiking in the mouse visual system reveals functional hierarchy," Nature, Nature, vol. 592(7852), pages 86-92, April.
- Youhui Zhang & Peng Qu & Yu Ji & Weihao Zhang & Guangrong Gao & Guanrui Wang & Sen Song & Guoqi Li & Wenguang Chen & Weimin Zheng & Feng Chen & Jing Pei & Rong Zhao & Mingguo Zhao & Luping Shi, 2020. "A system hierarchy for brain-inspired computing," Nature, Nature, vol. 586(7829), pages 378-384, October.
- Vladimir Gligorijević & P. Douglas Renfrew & Tomasz Kosciolek & Julia Koehler Leman & Daniel Berenberg & Tommi Vatanen & Chris Chandler & Bryn C. Taylor & Ian M. Fisk & Hera Vlamakis & Ramnik J. Xavie, 2021. "Structure-based protein function prediction using graph convolutional networks," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
- István A. Kovács & Katja Luck & Kerstin Spirohn & Yang Wang & Carl Pollis & Sadie Schlabach & Wenting Bian & Dae-Kyum Kim & Nishka Kishore & Tong Hao & Michael A. Calderwood & Marc Vidal & Albert-Lász, 2019. "Network-based prediction of protein interactions," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
- Leo Katz, 1953. "A new status index derived from sociometric analysis," Psychometrika, Springer;The Psychometric Society, vol. 18(1), pages 39-43, March.
- Tao Zhou & Linyuan Lü & Yi-Cheng Zhang, 2009. "Predicting missing links via local information," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 71(4), pages 623-630, October.
- John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
- Evi Hendrikx & Jacob M. Paul & Martijn Ackooij & Nathan Stoep & Ben M. Harvey, 2022. "Visual timing-tuned responses in human association cortices and response dynamics in early visual cortex," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Jiahua Rao & Jiancong Xie & Qianmu Yuan & Deqin Liu & Zhen Wang & Yutong Lu & Shuangjia Zheng & Yuedong Yang, 2024. "A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Xu-Wen Wang & Lorenzo Madeddu & Kerstin Spirohn & Leonardo Martini & Adriano Fazzone & Luca Becchetti & Thomas P. Wytock & István A. Kovács & Olivér M. Balogh & Bettina Benczik & Mátyás Pétervári & Be, 2023. "Assessment of community efforts to advance network-based prediction of protein–protein interactions," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
- Lee, Yan-Li & Zhou, Tao, 2021. "Collaborative filtering approach to link prediction," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 578(C).
- Zhou, Tao & Lee, Yan-Li & Wang, Guannan, 2021. "Experimental analyses on 2-hop-based and 3-hop-based link prediction algorithms," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 564(C).
- Yu, Jiating & Wu, Ling-Yun, 2022. "Multiple Order Local Information model for link prediction in complex networks," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 600(C).
- Stefanie Duller & Simone Vrbancic & Łukasz Szydłowski & Alexander Mahnert & Marcus Blohs & Michael Predl & Christina Kumpitsch & Verena Zrim & Christoph Högenauer & Tomasz Kosciolek & Ruth A. Schmitz , 2024. "Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Lee, Yan-Li & Dong, Qiang & Zhou, Tao, 2021. "Link prediction via controlling the leading eigenvector," Applied Mathematics and Computation, Elsevier, vol. 411(C).
- Aziz, Furqan & Gul, Haji & Muhammad, Ishtiaq & Uddin, Irfan, 2020. "Link prediction using node information on local paths," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 557(C).
- Yu, Jiating & Leng, Jiacheng & Sun, Duanchen & Wu, Ling-Yun, 2023. "Network Refinement: Denoising complex networks for better community detection," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 617(C).
- Julia Koehler Leman & Pawel Szczerbiak & P. Douglas Renfrew & Vladimir Gligorijevic & Daniel Berenberg & Tommi Vatanen & Bryn C. Taylor & Chris Chandler & Stefan Janssen & Andras Pataki & Nick Carrier, 2023. "Sequence-structure-function relationships in the microbial protein universe," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
- Marco Malatesta & Emanuele Fornasier & Martino Luigi Salvo & Angela Tramonti & Erika Zangelmi & Alessio Peracchi & Andrea Secchi & Eugenia Polverini & Gabriele Giachin & Roberto Battistutta & Roberto , 2024. "One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Simon L. Dürr & Andrea Levy & Ursula Rothlisberger, 2023. "Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins," Nature Communications, Nature, vol. 14(1), pages 1-14, 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.
- 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.
- 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.
- Pierre Azoulay & Joshua L. Krieger & Abhishek Nagaraj, 2024. "Old Moats for New Models: Openness, Control, and Competition in Generative AI," NBER Working Papers 32474, National Bureau of Economic Research, Inc.
- 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.
- 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.
- Bret M. Boyd & Ian James & Kevin P. Johnson & Robert B. Weiss & Sarah E. Bush & Dale H. Clayton & Colin Dale, 2024. "Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- 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.
- 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.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36736-1. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.