AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery

10 October 2015

Papers citing "AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery"

45 / 45 papers shown

Title
AI-Driven Automation Can Become the Foundation of Next-Era Science of Science Research Renqi Chen Haoyang Su Shixiang Tang Zhenfei Yin Qingbo Wu Hui Li Ye Sun Nanqing Dong Wanli Ouyang Philip Torr AI4CE 22 0 0 17 May 2025
Comparing Hyper-optimized Machine Learning Models for Predicting Efficiency Degradation in Organic Solar Cells David Valiente Fernando Rodríguez-Mas J. Alegre‐Requena David Dalmau María Flores J. Ferrer 20 0 0 29 Mar 2024
DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries Kirill Shmilovich Benson Chen Theofanis Karaletos Mohammad M. Sultan 19 12 0 30 Nov 2022
Drug-target affinity prediction method based on consistent expression of heterogeneous data Boyuan Liu 15 0 0 13 Nov 2022
An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries Aryan Pedawi P. Gniewek Chao-Ling Chang Brandon M. Anderson H. V. D. Bedem 41 5 0 19 Oct 2022
Learning Neural Set Functions Under the Optimal Subset Oracle Zijing Ou Tingyang Xu Qinliang Su Yingzhen Li P. Zhao Yatao Bian BDL 18 9 0 03 Mar 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 38 262 0 07 Feb 2022
Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networks C. Knutson Mridula Bontha Jenna A. Bilbrey Neeraj Kumar 22 34 0 30 Nov 2021
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking O. Ganea Xinyuan Huang Charlotte Bunne Yatao Bian Regina Barzilay Tommi Jaakkola Andreas Krause 36 152 0 15 Nov 2021
Improved Drug-target Interaction Prediction with Intermolecular Graph Transformer Siyuan Liu Yusong Wang Tong Wang Yifan Deng Liang He Jia Zhang Jian Yin Nanning Zheng Tie-Yan Liu 28 16 0 14 Oct 2021
Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity Shuangli Li Jingbo Zhou Tong Xu Liang Huang Fan Wang Haoyi Xiong Weili Huang Dejing Dou Hui Xiong MLAU 27 166 0 21 Jul 2021
SpreadGNN: Serverless Multi-task Federated Learning for Graph Neural Networks Chaoyang He Emir Ceyani Keshav Balasubramanian M. Annavaram Salman Avestimehr FedML 25 50 0 04 Jun 2021
A Novel Framework Integrating AI Model and Enzymological Experiments Promotes Identification of SARS-CoV-2 3CL Protease Inhibitors and Activity-based Probe F. Hu Lei Wang Yishen Hu Dongqi Wang Weijie Wang Jiaqiang Jiang Nan Li P. Yin 21 11 0 29 May 2021
An Oracle for Guiding Large-Scale Model/Hybrid Parallel Training of Convolutional Neural Networks A. Kahira Truong Thao Nguyen L. Bautista-Gomez Ryousei Takano Rosa M. Badia Mohamed Wahib 18 9 0 19 Apr 2021
Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models Tomohide Masuda Matthew Ragoza D. Koes DiffM 37 52 0 16 Oct 2020
Where Does Trust Break Down? A Quantitative Trust Analysis of Deep Neural Networks via Trust Matrix and Conditional Trust Densities Andrew Hryniowski Xiao Yu Wang A. Wong 25 10 0 30 Sep 2020
Drug discovery with explainable artificial intelligence José Jiménez-Luna F. Grisoni G. Schneider 30 626 0 01 Jul 2020
Self-Supervised Graph Transformer on Large-Scale Molecular Data Yu Rong Yatao Bian Tingyang Xu Wei-yang Xie Ying Wei Wenbing Huang Junzhou Huang AI4CE 24 25 0 18 Jun 2020
Improved Protein-ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference Derek Jones Hyojin Kim Xiaohua Zhang A. Zemla Garrett A. Stevenson W. D. Bennett D. Kirshner Sergio E. Wong F. Lightstone Jonathan E. Allen AI4CE 15 190 0 17 May 2020
Molecule Attention Transformer Lukasz Maziarka Tomasz Danel Slawomir Mucha Krzysztof Rataj Jacek Tabor Stanislaw Jastrzebski 19 168 0 19 Feb 2020
Combining Machine Learning with Knowledge-Based Modeling for Scalable Forecasting and Subgrid-Scale Closure of Large, Complex, Spatiotemporal Systems Alexander Wikner Jaideep Pathak Brian Hunt M. Girvan T. Arcomano I. Szunyogh Andrew Pomerance Edward Ott AI4CE 64 70 0 10 Feb 2020
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts Mostafa Karimi Di Wu Zhangyang Wang Yang Shen 27 46 0 29 Dec 2019
DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction Yanjun Li M. Rezaei Chenglong Li Xiaolin Li D. Wu 3DV 27 61 0 01 Dec 2019
Quantitative Verification of Neural Networks And its Security Applications Teodora Baluta Shiqi Shen Shweta Shinde Kuldeep S. Meel P. Saxena AAML 24 104 0 25 Jun 2019
SMILES-X: autonomous molecular compounds characterization for small datasets without descriptors G. Lambard Ekaterina Gracheva 27 20 0 20 Jun 2019
Efficient Toxicity Prediction via Simple Features Using Shallow Neural Networks and Decision Trees Abdul Karim Avinash Mishra M. A. Hakim Newton A. Sattar 21 55 0 26 Jan 2019
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models Daniil Polykovskiy Alexander Zhebrak Benjamín Sánchez-Lengeling Sergey Golovanov Oktai Tatanov ... Simon Johansson Hongming Chen Sergey I. Nikolenko Alán Aspuru-Guzik Alex Zhavoronkov ELM 206 633 0 29 Nov 2018
Three-Dimensionally Embedded Graph Convolutional Network (3DGCN) for Molecule Interpretation Hyeoncheol Cho I. Choi 30 55 0 24 Nov 2018
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images I. Cortés-Ciriano A. Bender MedIm 30 51 0 22 Nov 2018
Latent Molecular Optimization for Targeted Therapeutic Design Tristan Aumentado-Armstrong 15 41 0 05 Sep 2018
Multimodal Deep Neural Networks using Both Engineered and Learned Representations for Biodegradability Prediction Garrett B. Goh Khushmeen Sakloth Charles Siegel Abhinav Vishnu J. Pfaendtner HAI 28 11 0 13 Aug 2018
DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks Mostafa Karimi Di Wu Zhangyang Wang Yang Shen 35 358 0 20 Jun 2018
Visualizing Convolutional Neural Network Protein-Ligand Scoring Joshua E. Hochuli Alec Helbling Tamar Skaist Matthew Ragoza D. Koes FAtt 16 65 0 06 Mar 2018
Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds Nathaniel Thomas Tess E. Smidt S. Kearnes Lusann Yang Li Li Kai Kohlhoff Patrick F. Riley 3DPC 44 944 0 22 Feb 2018
A Spatial Mapping Algorithm with Applications in Deep Learning-Based Structure Classification T. Corcoran R. Zamora-Resendiz Xinlian Liu S. Crivelli 3DPC 3DV 18 16 0 07 Feb 2018
Adaptive Graph Convolutional Neural Networks Ruoyu Li Sheng Wang Feiyun Zhu Junzhou Huang GNN 26 747 0 10 Jan 2018
DGCNN: Disordered Graph Convolutional Neural Network Based on the Gaussian Mixture Model Bo Wu Yang Liu B. Lang Lei Huang 27 68 0 10 Dec 2017
Using Rule-Based Labels for Weak Supervised Learning: A ChemNet for Transferable Chemical Property Prediction Garrett B. Goh Charles Siegel Abhinav Vishnu Nathan Oken Hodas 21 90 0 07 Dec 2017
On-Chip Communication Network for Efficient Training of Deep Convolutional Networks on Heterogeneous Manycore Systems Wonje Choi Karthik Duraisamy R. Kim J. Doppa P. Pande Diana Marculescu R. Marculescu 21 66 0 05 Dec 2017
Ligand Pose Optimization with Atomic Grid-Based Convolutional Neural Networks Matthew Ragoza Lillian Turner D. Koes 32 16 0 20 Oct 2017
Learning Graph While Training: An Evolving Graph Convolutional Neural Network Ruoyu Li Junzhou Huang GNN 33 7 0 10 Aug 2017
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 260 1,789 0 02 Mar 2017
Learning Deep Architectures for Interaction Prediction in Structure-based Virtual Screening Adam Gonczarek Jakub M. Tomczak Szymon Zareba J. Kaczmar P. Dabrowski Michał J. Walczak 27 68 0 23 Oct 2016
Molecular Graph Convolutions: Moving Beyond Fingerprints S. Kearnes Kevin McCloskey Marc Berndl Vijay S. Pande Patrick F. Riley GNN 52 1,436 0 02 Mar 2016
Convolutional Rectifier Networks as Generalized Tensor Decompositions Nadav Cohen Amnon Shashua 20 152 0 01 Mar 2016