Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity

21 July 2021

Fan Wang

Haoyi Xiong

Papers citing "Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity"

47 / 47 papers shown

Title
PyTDC: A multimodal machine learning training, evaluation, and inference platform for biomedical foundation models Alejandro Velez-Arce Marinka Zitnik 24 0 0 08 May 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu J. Wu Q. Li Mingze Yin Jieping Ye Jian Wu Z. Wang 60 0 0 06 Mar 2025
DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking Jiaxian Yan Zaixi Zhang Jintao Zhu Kai Zhang Jianfeng Pei Qi Liu 26 2 0 15 Oct 2024
GUNDAM: Aligning Large Language Models with Graph Understanding Sheng Ouyang Yulan Hu Ge Chen Yong Liu AI4CE 31 3 0 30 Sep 2024
Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches Xuefeng Liu Songhao Jiang Xiaotian Duan Archit Vasan Chong Liu ... Heng Ma Thomas Brettin Fangfang Xia Ian T. Foster Rick L. Stevens AI4CE 31 0 0 30 Sep 2024
Improving generalisability of 3D binding affinity models in low data regimes Julia Buhmann Ward Haddadin Lukáš Pravda Alan Bilsland Hagen Triendl AI4CE 28 0 0 19 Sep 2024
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction Rong Han Xiaohong Liu Tong Pan Jing Xu Xiaoyu Wang ... Zhenyu Li Zixuan Wang Jiangning Song Guangyu Wang Ting Chen 24 0 0 21 Aug 2024
Barlow Twins Deep Neural Network for Advanced 1D Drug-Target Interaction Prediction Maximilian G. Schuh Davide Boldini Annkathrin I. Bohne Stephan A. Sieber 28 0 0 31 Jul 2024
Graph Neural Networks: A suitable Alternative to MLPs in Latent 3D Medical Image Classification? Johannes Kiechle Daniel M. Lang Stefan M. Fischer Lina Felsner J. Peeken Julia A. Schnabel MedIm 32 0 0 24 Jul 2024
SPIN: SE(3)-Invariant Physics Informed Network for Binding Affinity Prediction Seungyeon Choi Sangmin Seo Sanghyun Park 32 0 0 10 Jul 2024
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance? Y. Tan Lirong Zheng Bozitao Zhong Liang Hong Bingxin Zhou 35 4 0 28 Jun 2024
Graph Neural Networks in Histopathology: Emerging Trends and Future Directions Siemen Brussee Giorgio Buzzanca Anne M.R. Schrader Jesper Kers 58 8 0 18 Jun 2024
HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning Rong Han Wenbing Huang Lingxiao Luo Xinyan Han Jiaming Shen Zhiqiang Zhang Jun Zhou Ting Chen 33 2 0 02 Apr 2024
Rethinking Propagation for Unsupervised Graph Domain Adaptation Meihan Liu Zeyu Fang Zhen Zhang Ming Gu Sheng Zhou Xin Eric Wang Jiajun Bu AI4CE 42 14 0 08 Feb 2024
Enhancing Neural Subset Selection: Integrating Background Information into Set Representations Binghui Xie Yatao Bian Kaiwen Zhou Yongqiang Chen Peilin Zhao Bo Han Wei Meng James Cheng 21 1 0 05 Feb 2024
Large Language Models as Topological Structure Enhancers for Text-Attributed Graphs Shengyin Sun Yuxiang Ren Chen Ma Xuecang Zhang 110 20 0 24 Nov 2023
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems Shuo-feng Zhang Yang Liu Lei Xie AI4CE GNN PINN 31 10 0 19 Nov 2023
Protein-ligand binding representation learning from fine-grained interactions Shikun Feng Minghao Li Yinjun Jia Wei-Ying Ma Yanyan Lan SSL AI4CE 21 8 0 09 Nov 2023
ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking Yi Yi Xu Wan Yatao Bian Ou-Yang Le Peilin Zhao 21 3 0 12 Oct 2023
HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery Alvaro Prat Hisham Abdel-Aty Gintautas Kamuntavicius Tanya Paquet P. Norvaisas Piero Gasparotto Roy Tal 23 2 0 22 Sep 2023
Deep Prompt Tuning for Graph Transformers Reza Shirkavand Heng-Chiao Huang 23 7 0 18 Sep 2023
BeeTLe: A Framework for Linear B-Cell Epitope Prediction and Classification Xiao Yuan 24 3 0 05 Sep 2023
An Experimental Comparison of Partitioning Strategies for Distributed Graph Neural Network Training Nikolai Merkel Daniel Stoll R. Mayer Hans-Arno Jacobsen GNN 19 1 0 29 Aug 2023
Building explainable graph neural network by sparse learning for the drug-protein binding prediction Yang Wang Zanyu Shi Timothy W. Richardson Kun Huang P. Weerawarna Yijie Wang 23 0 0 27 Aug 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 32 1 0 20 Jun 2023
Multi-Temporal Relationship Inference in Urban Areas Shuangli Li Jingbo Zhou Ji Liu Tong Bill Xu Enhong Chen Hui Xiong 27 3 0 15 Jun 2023
Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction Jiaxian Yan Zhaofeng Ye Ziyi Yang Chengqiang Lu Shengyu Zhang Qi Liu J. Qiu 35 11 0 08 Jun 2023
Graph Neural Networks can Recover the Hidden Features Solely from the Graph Structure Ryoma Sato 34 5 0 26 Jan 2023
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction Gregory W. Kyro Rafael I. Brent Victor S. Batista 17 35 0 23 Dec 2022
Distributed Graph Neural Network Training: A Survey Yingxia Shao Hongzheng Li Xizhi Gu Hongbo Yin Yawen Li Xupeng Miao Wentao Zhang Bin Cui Lei Chen GNN AI4CE 11 56 0 01 Nov 2022
Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Network Yi Yi Xu Wan Kangfei Zhao Ou-Yang Le Pei-Ying Zhao 21 1 0 27 Oct 2022
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 51 104 0 19 Oct 2022
Predicting Protein-Ligand Binding Affinity via Joint Global-Local Interaction Modeling Yang Zhang G. Zhou Zhewei Wei Hongteng Xu 27 9 0 18 Sep 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 45 20 0 12 Sep 2022
From Static to Dynamic Structures: Improving Binding Affinity Prediction with a Graph-Based Deep Learning Model Yaosen Min Ye Wei Peizhuo Wang Xiao-tong Wang Han Li ... Yu Shi Yingheng Wang Ji Wu Dan Zhao Jianyang Zeng AI4CE 13 2 0 19 Aug 2022
Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes Shuo-feng Zhang Yang Liu Lei Xie GNN AI4CE 25 12 0 06 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 25 32 0 25 May 2022
High Performance of Gradient Boosting in Binding Affinity Prediction Dmitrii Gavrilev Nurlybek Amangeldiuly Sergei Ivanov Evgeny Burnaev AI4CE 25 2 0 14 May 2022
Compound virtual screening by learning-to-rank with gradient boosting decision tree and enrichment-based cumulative gain Kairi Furui Masahito Ohue 6 6 0 04 May 2022
Graph Pooling for Graph Neural Networks: Progress, Challenges, and Opportunities Chuang Liu Yibing Zhan Jia Wu Chang Li Bo Du Wenbin Hu Tongliang Liu Dacheng Tao GNN AI4CE 30 79 0 15 Apr 2022
Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy Binjie Guo Hanyu Zheng Haohan Jiang Xiaodan Li Nai-Yang Guan Yanming Zuo Yicheng Zhang Hengfu Yang Xuhua Wang 14 4 0 30 Mar 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
Learning Neural Set Functions Under the Optimal Subset Oracle Zijing Ou Tingyang Xu Qinliang Su Yingzhen Li P. Zhao Yatao Bian BDL 16 9 0 03 Mar 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 63 73 0 24 Jan 2022
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 30 151 0 15 Nov 2021
GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction Shuangli Li Jingbo Zhou Tong Bill Xu Dejing Dou Hui Xiong AI4CE 28 118 0 24 Sep 2021