Structure-based drug design with geometric deep learning

19 October 2022

Papers citing "Structure-based drug design with geometric deep learning"

31 / 31 papers shown

Title
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule Keyue Qiu Yuxuan Song Zhehuan Fan Peidong Liu Z. Zhang Mingyue Zheng Hao Zhou Wei-Ying Ma 11 0 0 12 May 2025
TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design Xiuyuan Hu Guoqing Liu Can Chen Yang Zhao Hao Zhang Xue Liu 44 2 0 26 Mar 2025
Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation Taojie Kuang Qianli Ma Athanasios V. Vasilakos Yu Wang Qiang Cheng Zhixiang Ren 38 0 0 11 Mar 2025
Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model G. Li Chenran Jiang Ziqi Gao Yu Liu Chenyang Liu Jiean Chen Yong Huang Jia Li 44 0 0 02 Mar 2025
Dockformer: A transformer-based molecular docking paradigm for large-scale virtual screening Zhangfan Yang Junkai Ji Shan He Jianqiang Li Ruibin Bai Zexuan Zhu Yew-Soon Ong Y. Ong 18 0 0 11 Nov 2024
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models Kiwoong Yoo Owen Oertell Junhyun Lee Sanghoon Lee Jaewoo Kang 31 0 0 28 Oct 2024
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics Chenqing Hua Yong Liu Dinghuai Zhang Odin Zhang Sitao Luan Kevin K. Yang Guy Wolf Doina Precup Shuangjia Zheng 14 4 0 01 Oct 2024
CW-CNN & CW-AN: Convolutional Networks and Attention Networks for CW-Complexes Rahul Khorana 21 0 0 29 Aug 2024
Reactzyme: A Benchmark for Enzyme-Reaction Prediction Chenqing Hua Bozitao Zhong Sitao Luan Liang Hong Guy Wolf Doina Precup Shuangjia Zheng 19 5 0 24 Aug 2024
MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space Yanru Qu Keyue Qiu Yuxuan Song Jingjing Gong Jiawei Han Mingyue Zheng Hao Zhou Wei-Ying Ma 28 18 0 18 Apr 2024
CADReN: Contextual Anchor-Driven Relational Network for Controllable Cross-Graphs Node Importance Estimation Zijie Zhong Yunhui Zhang Ziyi Chang Zengchang Qin GNN 6 0 0 06 Feb 2024
Effective Protein-Protein Interaction Exploration with PPIretrieval Chenqing Hua Connor W. Coley Guy Wolf Doina Precup Shuangjia Zheng 8 3 0 06 Feb 2024
Quantum-Inspired Machine Learning for Molecular Docking Runqiu Shu Bowen Liu Zhaoping Xiong Xiaopeng Cui Yunting Li Wei Cui Manhong Yung Nan Qiao 6 1 0 22 Jan 2024
A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systems Shuo-feng Zhang Yang Liu Lei Xie AI4CE GNN PINN 16 9 0 19 Nov 2023
AtomSurf : Surface Representation for Learning on Protein Structures Vincent Mallet Souhaib Attaiki M. Ovsjanikov 19 3 0 28 Sep 2023
MoleCLUEs: Molecular Conformers Maximally In-Distribution for Predictive Models Michael R. Maser Natasa Tagasovska Jae Hyeon Lee Andrew Watkins 19 0 0 20 Jun 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 17 1 0 20 Jun 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Zhiling Zheng ... Anima Anandkumar C. Borgs J. Chayes Hongyu Guo Jian Tang AI4CE 26 17 0 15 Jun 2023
Geometric Epitope and Paratope Prediction Marco Pegoraro Clémentine Dominé Emanuele Rodolà Petar Velickovic Andreea Deac 17 2 0 28 May 2023
Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach G. Palermo Gianmarco Accordi Davide Gadioli Emanuele Vitali Cristina Silvano ... Eric Lindahl D. Gregori Emanuele Sana Silvano Coletti P. Gschwandtner ELM 11 5 0 19 Apr 2023
Learning Harmonic Molecular Representations on Riemannian Manifold Yiqun Wang Yuning Shen Shih‐Ya Chen Lihao Wang Fei Ye Hao Zhou 16 7 0 27 Mar 2023
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction Yang Zhang Zhewei Wei Yefei Yuan Zhaohan Ding Wenbing Huang 8 10 0 23 Feb 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 130 399 0 04 Oct 2022
Accurate Machine Learned Quantum-Mechanical Force Fields for Biomolecular Simulations Oliver T. Unke M. Stohr Stefan Ganscha Thomas Unterthiner Hartmut Maennel ... Daniel Ahlin M. Gastegger L. M. Sandonas A. Tkatchenko Klaus-Robert Muller AI4CE 16 18 0 17 May 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 60 176 0 20 Mar 2022
Geometric Transformers for Protein Interface Contact Prediction Alex Morehead Chen Chen Jianlin Cheng 23 28 0 06 Oct 2021
Inverse design of 3d molecular structures with conditional generative neural networks Niklas W. A. Gebauer M. Gastegger Stefaan S. P. Hessmann Klaus-Robert Muller Kristof T. Schütt AI4CE 173 125 0 10 Sep 2021
SpookyNet: Learning Force Fields with Electronic Degrees of Freedom and Nonlocal Effects Oliver T. Unke Stefan Chmiela M. Gastegger Kristof T. Schütt H. E. Sauceda K. Müller 142 242 0 01 May 2021
Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges M. Bronstein Joan Bruna Taco S. Cohen Petar Velivcković GNN 161 1,095 0 27 Apr 2021
E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials Simon L. Batzner Albert Musaelian Lixin Sun Mario Geiger J. Mailoa M. Kornbluth N. Molinari Tess E. Smidt Boris Kozinsky 183 1,218 0 08 Jan 2021
Geometric deep learning: going beyond Euclidean data M. Bronstein Joan Bruna Yann LeCun Arthur Szlam P. Vandergheynst GNN 228 3,202 0 24 Nov 2016