DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks

20 June 2018

Papers citing "DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks"

50 / 53 papers shown

Title
Rethinking the generalization of drug target affinity prediction algorithms via similarity aware evaluation Chenbin Zhang Zhiqiang Hu Chuchu Jiang Wen Chen Jie Xu S. Zhang 30 0 0 13 Apr 2025
SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction Y. Chen Xiang Ji Ziyue Zhang Yuming Zhou Yang-Chi-Dung Lin ... Yixian Huang Shidong Cui Shih-Chung Yen Ariel Warshel Hsien-Da Huang 64 0 0 12 Mar 2025
Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A Hemagglutinin Ella Barkan Ibrahim Siddiqui Kevin J. Cheng Alex Golts Yoel Shoshan J. Weber Yailin Campos Mota Michal Ozery-Flato Giuseppe A. Sautto AI4CE 56 0 0 02 Feb 2025
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors Qizhi Pei Lijun Wu Zhenyu He Jinhua Zhu Yingce Xia Shufang Xie Rui Yan 29 0 0 21 Jul 2024
Towards Understanding Sensitive and Decisive Patterns in Explainable AI: A Case Study of Model Interpretation in Geometric Deep Learning Jiajun Zhu Siqi Miao Rex Ying Pan Li 40 1 0 30 Jun 2024
How Interpretable Are Interpretable Graph Neural Networks? Yongqiang Chen Yatao Bian Bo Han James Cheng 49 4 0 12 Jun 2024
DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms Zhangli Lu Chuqi Lei Kaili Wang Libo Qin Jing Tang Min Li 16 1 0 23 Dec 2023
XAI meets Biology: A Comprehensive Review of Explainable AI in Bioinformatics Applications Zhongliang Zhou Mengxuan Hu Mariah Salcedo Nathan Gravel Wayland Yeung Aarya Venkat Dongliang Guo Jielu Zhang N. Kannan Sheng Li 14 6 0 11 Dec 2023
Protein-ligand binding representation learning from fine-grained interactions Shikun Feng Minghao Li Yinjun Jia Wei-Ying Ma Yanyan Lan SSL AI4CE 24 8 0 09 Nov 2023
FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation Ali Khodabandeh Yalabadi Mehdi Yazdani-Jahromi Niloofar Yousefi Aida Tayebi Sina Abdidizaji O. Garibay 10 2 0 04 Nov 2023
Learning Invariant Molecular Representation in Latent Discrete Space Zhuang Xiang Qiang Zhang Keyan Ding Yatao Bian Xiao Wang Jingsong Lv Hongyang Chen Huajun Chen OOD 26 16 0 22 Oct 2023
ProFSA: Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment Bowen Gao Yinjun Jia Yuanle Mo Yuyan Ni Wei-Ying Ma Zhiming Ma Yanyan Lan 22 7 0 11 Oct 2023
Explainable AI applications in the Medical Domain: a systematic review Nicoletta Prentzas A. Kakas Constantinos S. Pattichis 16 11 0 10 Aug 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 35 0 0 05 Apr 2023
A Brief Review of Explainable Artificial Intelligence in Healthcare Zahra Sadeghi R. Alizadehsani M. Cifci Samina Kausar Rizwan Rehman ... A. Shoeibi H. Moosaei Milan Hladík Saeid Nahavandi P. Pardalos 19 13 0 04 Apr 2023
AmorProt: Amino Acid Molecular Fingerprints Repurposing based Protein Fingerprint Myeong-Sung Lee K. Min 16 1 0 27 Mar 2023
Interpretable machine learning of amino acid patterns in proteins: a statistical ensemble approach A. Braghetto E. Orlandini M. Baiesi 32 4 0 27 Mar 2023
Structure-based drug discovery with deep learning Rıza Özçelik D. V. Tilborg José Jiménez-Luna F. Grisoni AI4CE 21 35 0 26 Dec 2022
Dynamic Molecular Graph-based Implementation for Biophysical Properties Prediction C. Knutson G. Panapitiya R. Varikoti Neeraj Kumar AI4CE 17 0 0 20 Dec 2022
Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks Fang Wu Yujun Tao Dragomir R. Radev Jinbo Xu Stan Z. Li AI4CE 30 32 0 07 Dec 2022
Quality-diversity in dissimilarity spaces Steve Huntsman 22 1 0 14 Nov 2022
Recent Developments in Structure-Based Virtual Screening Approaches C. Gorgulla 16 0 0 06 Nov 2022
Geometry-Complete Perceptron Networks for 3D Molecular Graphs Alex Morehead Jianlin Cheng GNN 3DV AI4CE 29 12 0 04 Nov 2022
Interpretable Geometric Deep Learning via Learnable Randomness Injection Siqi Miao Yunan Luo Miaoyuan Liu Pan Li 24 25 0 30 Oct 2022
Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space Gian Marco Visani Michael N. Pun Arman Angaji Armita Nourmohammad BDL 24 3 0 30 Sep 2022
ImDrug: A Benchmark for Deep Imbalanced Learning in AI-aided Drug Discovery Lanqing Li Li Zeng Zi-Chao Gao Shen Yuan Yatao Bian ... Wei Liu Hongteng Xu Jia Li P. Zhao Pheng-Ann Heng VLM 26 4 0 16 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 45 20 0 12 Sep 2022
SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction Qizhi Pei Lijun Wu Jinhua Zhu Yingce Xia Shufang Xia Tao Qin Haiguang Liu Tie-Yan Liu Rui Yan 13 20 0 20 Jun 2022
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding Minghao Xu Zuobai Zhang Jiarui Lu Zhaocheng Zhu Yang Zhang Chang Ma Runcheng Liu Jian Tang 11 98 0 05 Jun 2022
SS-GNN: A Simple-Structured Graph Neural Network for Affinity Prediction Shuke Zhang Yan Jin Tianmeng Liu Qi Wang Zhaohui Zhang Shuliang Zhao Bo Shan 27 32 0 25 May 2022
Associative Learning Mechanism for Drug-Target Interaction Prediction Zhiqin Zhu Zheng Yao Guanqiu Qi Neal Mazur Baisheng Cong OOD 14 30 0 24 May 2022
Accelerating Inhibitor Discovery With A Deep Generative Foundation Model: Validation for SARS-CoV-2 Drug Targets Vijil Chenthamarakshan Samuel C. Hoffman C. Owen P. Lukacik C. Strain-Damerell ... Aleksandra Mojsilović J. Crain Martin A. Walsh David I. Stuart Payel Das 20 0 0 19 Apr 2022
Hierarchical Graph Representation Learning for the Prediction of Drug-Target Binding Affinity Zhaoyang Chu Shichao Liu Wen Zhang 25 40 0 22 Mar 2022
Target-aware Molecular Graph Generation Cheng Tan Zhangyang Gao Stan Z. Li 24 25 0 10 Feb 2022
Deep learning for drug repurposing: methods, databases, and applications Xiao Pan Xuan Lin Dongsheng Cao Xiangxiang Zeng Philip S. Yu Lifang He R. Nussinov F. Cheng 25 126 0 08 Feb 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 22 262 0 07 Feb 2022
DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations Yuanfeng Ji Lu Zhang Jiaxiang Wu Bing Wu Long-Kai Huang ... Ping Luo Shuigeng Zhou Junzhou Huang Peilin Zhao Yatao Bian OOD 66 73 0 24 Jan 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
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology Tian Cai Li Xie Muge Chen Yang Liu Di He Shuo-feng Zhang C. Mura P. Bourne Lei Xie OOD 21 4 0 23 Nov 2021
Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs Fang Wu Dragomir R. Radev Huabin Xing ViT 36 54 0 04 Oct 2021
MLIMC: Machine learning-based implicit-solvent Monte Carlo Jiahui Chen Weihua Geng G. Wei 14 10 0 24 Sep 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 34 287 0 26 Jul 2021
PyKale: Knowledge-Aware Machine Learning from Multiple Sources in Python Haiping Lu Xianyuan Liu Robert Turner Peizhen Bai Raivo Koot Shuo Zhou Mustafa Chasmai Lawrence Schobs 25 4 0 17 Jun 2021
ParaVS: A Simple, Fast, Efficient and Flexible Graph Neural Network Framework for Structure-Based Virtual Screening Junfeng Wu Dawei Leng Lurong Pan 13 0 0 08 Feb 2021
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction QHwan Kim Joon-Hyuk Ko Sunghoon Kim Nojun Park W. Jhe BDL 32 27 0 15 Dec 2020
ATOM3D: Tasks On Molecules in Three Dimensions Raphael J. L. Townshend M. Vögele Patricia Suriana Alexander Derry Alexander Powers ... Brandon M. Anderson Stephan Eismann Risi Kondor Russ Altman R. Dror AI4CE 19 118 0 07 Dec 2020
Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact Prediction Yuning You Yang Shen 25 8 0 14 Nov 2020
$PaccMann$^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models$ PaccMann $^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models Jannis Born Matteo Manica Joris Cadow Greta Markert N. Mill Modestas Filipavicius María Rodríguez Martínez 21 4 0 27 May 2020
Network-principled deep generative models for designing drug combinations as graph sets Mostafa Karimi Arman Hasanzadeh Yang Shen GNN 19 31 0 16 Apr 2020
CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models Vijil Chenthamarakshan Payel Das Samuel C. Hoffman Hendrik Strobelt Inkit Padhi ... Benjamin Hoover Matteo Manica Jannis Born Teodoro Laino Aleksandra Mojsilović 37 41 0 02 Apr 2020