3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction

6 March 2023

Papers citing "3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction"

44 / 94 papers shown

Title
Structure-based drug design by denoising voxel grids Pedro H. O. Pinheiro Arian R. Jamasb Omar Mahmood Vishnu Sresht Saeed Saremi DiffM 39 8 0 07 May 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes BDL DiffM 46 11 0 30 Apr 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 35 18 0 18 Apr 2024
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design Xinze Li Penglei Wang Tianfan Fu Wenhao Gao Chengtao Li Leilei Shi Junhong Liu 48 2 0 02 Apr 2024
CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability Gregory W. Kyro Matthew T. Martin Eric D. Watt Victor S. Batista 43 2 0 12 Mar 2024
DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization Xiangxin Zhou Xiwei Cheng Yuwei Yang Yu Bao Liang Wang Quanquan Gu 44 15 0 07 Mar 2024
Stabilizing Policy Gradients for Stochastic Differential Equations via Consistency with Perturbation Process Xiangxin Zhou Liang Wang Yichi Zhou DiffM 32 4 0 07 Mar 2024
PPFlow: Target-aware Peptide Design with Torsional Flow Matching Haitao Lin Odin Zhang Huifeng Zhao Dejun Jiang Lirong Wu Zicheng Liu Yufei Huang Stan Z. Li 57 12 0 05 Mar 2024
Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion Bowen Gao Minsi Ren Yuyan Ni Yanwen Huang Yiran Zhou Zhiming Ma Wei-Ying Ma Yanyan Lan 39 4 0 04 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 34 20 0 01 Mar 2024
DecompDiff: Diffusion Models with Decomposed Priors for Structure-Based Drug Design Jiaqi Guan Xiangxin Zhou Yuwei Yang Yu Bao Jian-wei Peng Jianzhu Ma Qiang Liu Liang Wang Quanquan Gu 40 68 0 26 Feb 2024
MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 36 4 0 16 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 24 25 0 13 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 32 0 0 28 Jan 2024
A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Vignesh C. Bhethanabotla ... O. Yaghi C. Borgs A. Anandkumar Hongyu Guo J. Chayes AI4CE 32 4 0 26 Jan 2024
FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction Alexander Telepov Artem Tsypin Kuzma Khrabrov Sergey Yakukhnov Pavel Strashnov ... Egor Rumiantsev Daniel Ezhov Manvel Avetisian Olga Popova Artur Kadurin 27 4 0 18 Jan 2024
Binding-Adaptive Diffusion Models for Structure-Based Drug Design Zhilin Huang Ling Yang Zaixi Zhang Xiangxin Zhou Yu Bao Xiawu Zheng Yuwei Yang Yu Wang Wenming Yang DiffM 45 8 0 15 Jan 2024
CoCoGen: Physically-Consistent and Conditioned Score-based Generative Models for Forward and Inverse Problems Christian L. Jacobsen Yilin Zhuang Karthik Duraisamy AI4CE SyDa DiffM 26 17 0 16 Dec 2023
Autoregressive fragment-based diffusion for pocket-aware ligand design Mahdi Ghorbani Leo Gendelev Paul Beroza Michael J. Keiser DiffM 31 8 0 15 Dec 2023
Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods Minsi Ren Bowen Gao Yiran Zhou Yanyan Lan 12 0 0 01 Nov 2023
TacoGFN: Target-conditioned GFlowNet for Structure-based Drug Design Tony Shen Seonghwan Seo Grayson Lee Mohit Pandey Jason R. Smith Artem Cherkasov Woo Youn Kim Martin Ester 94 0 0 05 Oct 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 27 25 0 29 Sep 2023
Distilling ODE Solvers of Diffusion Models into Smaller Steps Sanghwan Kim Hao Tang Fisher Yu 20 3 0 28 Sep 2023
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models Ziqi Chen B. Peng Srinivas Parthasarathy Xia Ning DiffM 36 11 0 23 Aug 2023
Diffusion probabilistic models enhance variational autoencoder for crystal structure generative modeling T. Pakornchote Natthaphon Choomphon-anomakhun Sorrjit Arrerut C. Atthapak S. Khamkaeo Thiparat Chotibut T. Bovornratanaraks DiffM 29 17 0 04 Aug 2023
Target-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning Haoxiang Luo Gang Sun 37 2 0 02 Aug 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 29 7 0 26 Jun 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
3D molecule generation by denoising voxel grids Pedro H. O. Pinheiro Joshua Rackers J. Kleinhenz Michael R. Maser Omar Mahmood Andrew Watkins Stephen Ra Vishnu Sresht Saeed Saremi DiffM 34 20 0 13 Jun 2023
On the Design Fundamentals of Diffusion Models: A Survey Ziyi Chang G. Koulieris Hubert P. H. Shum DiffM 29 53 0 07 Jun 2023
Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration Haitao Lin Yufei Huang Haotian Zhang Lirong Wu Siyuan Li Zhiyuan Chen Stan Z. Li DiffM 19 23 0 30 May 2023
Generation of 3D Molecules in Pockets via Language Model Wei Feng L. Wang Zaiyun Lin Yanhao Zhu Han Wang ... Huting Wang Jielong Zhou Wei Peng Bo Huang Wenbiao Zhou 33 12 0 17 May 2023
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng Jiaqi Guan Qiang Liu Jianzhu Ma DiffM 33 43 0 11 May 2023
3D Molecular Generation via Virtual Dynamics Shuqi Lu Lin Yao X. Chen Hang Zheng Di He Guolin Ke DiffM 26 7 0 12 Feb 2023
Geometry-Complete Diffusion for 3D Molecule Generation and Optimization Alex Morehead Jianlin Cheng DiffM 14 23 0 08 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications Junfeng Fang Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 32 58 0 06 Feb 2023
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lió Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 42 195 0 24 Oct 2022
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 53 104 0 19 Oct 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 224 1,304 0 02 Sep 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 67 178 0 20 Mar 2022
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions Emiel Hoogeboom Didrik Nielsen P. Jaini Patrick Forré Max Welling DiffM 207 394 0 10 Feb 2021
Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models Matthew Ragoza Tomohide Masuda D. Koes DiffM MedIm 75 31 0 17 Oct 2020
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 206 885 0 07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 224 1,340 0 12 Feb 2018