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Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery.
Hierarchical recurrent neural networks for long-term dependencies
Salah El Hihi and Yoshua Bengio · 1996
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Can the pharmaceutical industry reduce attrition rates?
Ismail Kola and John Landis · 2004
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Bindingdb: a web-accessible database of experimentally determined protein–ligand binding affinities
Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N Jorissen, and Michael K Gilson · 2007
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How to improve r&d productivity: the pharmaceutical industry’s grand challenge
Steven M Paul, Daniel S Mytelka, Christopher T Dunwiddie, Charles C Persinger, Bernard H Munos, Stacy R Lindborg, and Aaron L Schacht · 2010
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Pdb-wide collection of binding data: current status of the pdbbind database
Zhihai Liu, Yan Li, Li Han, Jie Li, Jie Liu, Zhixiong Zhao, Wei Nie, Yuchen Liu, and Renxiao Wang · 2015
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Atomic convolutional networks for predicting protein-ligand binding affinity
Joseph Gomes, Bharath Ramsundar, Evan N Feinberg, and Vijay S Pande · 2017
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Petar Veličković, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Lio, and Yoshua Bengio · 2017
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Accurate de novo prediction of protein contact map by ultra-deep learning model
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, and Jinbo Xu · 2017
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Inductive representation learning on large graphs
Will Hamilton, Zhitao Ying, and Jure Leskovec · 2017
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KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
J. Jimenez, M. Skalic, G. Martinez-Rosell, and G. De Fabritiis · 2018
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Deepdta: deep drug–target binding affinity prediction
Hakime Öztürk, Arzucan Özgür, and Elif Ozkirimli · 2018
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Interpretable drug target prediction using deep neural representation
Kyle Yingkai Gao, Achille Fokoue, Heng Luo, Arun Iyengar, Sanjoy Dey, and Ping Zhang · 2018
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Pdbsum: Structural summaries of pdb entries
Roman A Laskowski, Jagoda Jabłońska, Lukáš Pravda, Radka Svobodová Vařeková, and Janet M Thornton · 2018
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How powerful are graph neural networks?
Keyulu Xu, Weihua Hu, Jure Leskovec, and Stefanie Jegelka · 2018
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Predicting drug–target interaction using a novel graph neural network with 3d structure-embedded graph representation
Jaechang Lim, Seongok Ryu, Kyubyong Park, Yo Joong Choe, Jiyeon Ham, and Woo Youn Kim · 2019
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Lxmert: Learning cross-modality encoder representations from transformers
Hao Tan and Mohit Bansal · 2019
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Drug–target affinity prediction using graph neural network and contact maps
Mingjian Jiang, Zhen Li, Shugang Zhang, Shuang Wang, Xiaofeng Wang, Qing Yuan, and Zhiqiang Wei · 2020
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Monn: A multi-objective neural network for predicting compound-protein interactions and affinities
Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, and Jianyang Zeng · 2020
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L 2 -gcn: Layer-wise and learned efficient training of graph convolutional networks
Yuning You, Tianlong Chen, Zhangyang Wang, and Yang Shen · 2020
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When does self-supervision help graph convolutional networks?
Yuning You, Tianlong Chen, Zhangyang Wang, and Yang Shen · 2020
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Graph Convolutional Neural Networks for Predicting Drug-Target Interactions
W. Torng and R. B. Altman · 2019
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Deepaffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks
Mostafa Karimi, Di Wu, Zhangyang Wang, and Yang Shen · 2019
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Compound–protein interaction prediction with end-to-end learning of neural networks for graphs and sequences
Masashi Tsubaki, Kentaro Tomii, and Jun Sese · 2019
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Explainable deep relational networks for predicting compound-protein affinities and contacts
Mostafa Karimi, Di Wu, Zhangyang Wang, and Yang Shen · 2019
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Graph contrastive learning with augmentations, 2020
Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, and Yang Shen · 2020
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Towards deeper graph neural networks
Meng Liu, Hongyang Gao, and Shuiwang Ji · 2020
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Adversarial attacks and defenses on graphs: A review and empirical study
Wei Jin, Yaxin Li, Han Xu, Yiqi Wang, and Jiliang Tang · 2020
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Energy-based graph convolutional networks for scoring protein docking models
Y. Cao and Y. Shen · 2020
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