DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding

21 November 2022

Lirong Wu

Stan Z. Li

Papers citing "DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding"

45 / 45 papers shown

Title
A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization Anjie Qiao Hao Zhang Qianmu Yuan Qirui Deng Jingtian Su W. R. Huang Huihao Zhou Guo-Bo Li Z. Wang J. Lei DiffM 31 0 0 09 May 2025
A 3D pocket-aware and affinity-guided diffusion model for lead optimization Anjie Qiao Junjie Xie W. R. Huang Hao Zhang Jiahua Rao Shuangjia Zheng Yuedong Yang Z. Wang Guo-Bo Li J. Lei DiffM MedIm 38 0 0 29 Apr 2025
Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation Taojie Kuang Qianli Ma Athanasios V. Vasilakos Yu Wang Qiang Cheng Zhixiang Ren 48 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 46 0 0 02 Mar 2025
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Ali Khodabandeh Yalabadi Mehdi Yazdani-Jahromi O. Garibay 39 0 0 28 Jan 2025
LMDM:Latent Molecular Diffusion Model For 3D Molecule Generation Xiang Chen DiffM 74 0 0 05 Dec 2024
Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design Xiangxin Zhou Jiaqi Guan Y. Zhang Xingang Peng Liang Wang Jianzhu Ma 26 2 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 31 5 0 01 Oct 2024
Decomposed Direct Preference Optimization for Structure-Based Drug Design Xiwei Cheng Xiangxin Zhou Yuwei Yang Yu Bao Quanquan Gu 38 3 0 19 Jul 2024
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph Haitao Lin Guojiang Zhao Odin Zhang Yufei Huang Lirong Wu Zicheng Liu Siyuan Li Cheng Tan Zhifeng Gao Stan Z. Li 29 3 0 16 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabás Póczos Newell Washburn MedIm 36 13 0 07 Jun 2024
BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning Artem Zholus Maksim Kuznetsov Roman Schutski Rim Shayakhmetov Daniil Polykovskiy Sarath Chandar Alex Zhavoronkov DiffM AI4CE 40 4 0 06 Jun 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 87 1 0 20 May 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 37 8 0 19 May 2024
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design Xinze Li Penglei Wang Tianfan Fu Wenhao Gao Chengtao Li Leilei Shi Junhong Liu 41 2 0 02 Apr 2024
Unified Generative Modeling of 3D Molecules via Bayesian Flow Networks Yuxuan Song Jingjing Gong Yanru Qu Hao Zhou Mingyue Zheng Jingjing Liu Wei-Ying Ma 33 10 0 17 Mar 2024
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation Odin Zhang Yufei Huang Shichen Cheng Mengyao Yu Xujun Zhang ... Yu Kang Sunliang Cui P. Pan Chang-Yu Hsieh Tingjun Hou 32 4 0 15 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 34 15 0 07 Mar 2024
Stabilizing Policy Gradients for Stochastic Differential Equations via Consistency with Perturbation Process Xiangxin Zhou Liang Wang Yichi Zhou DiffM 24 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 49 12 0 05 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 27 68 0 26 Feb 2024
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge Yufei Huang Odin Zhang Lirong Wu Cheng Tan Haitao Lin Zhangyang Gao Siyuan Li Stan. Z. Li DiffM 24 6 0 18 Feb 2024
Zero Shot Molecular Generation via Similarity Kernels Rokas Elijosius Fabian Zills Ilyes Batatia Sam Walton Norwood D. P. Kovács Christian Holm Gábor Csányi DiffM 41 3 0 13 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 26 0 0 28 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 37 8 0 15 Jan 2024
Equivariant Flow Matching with Hybrid Probability Transport Yuxuan Song Jingjing Gong Minkai Xu Ziyao Cao Yanyan Lan Stefano Ermon Hao Zhou Wei-Ying Ma DiffM 28 45 0 12 Dec 2023
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction Yufei Huang Siyuan Li Jin Su Lirong Wu Odin Zhang ... Zihan Liu Zhangyang Gao Yuyang Liu Jiangbin Zheng Stan. ZQ. Li 3DV 38 13 0 14 Oct 2023
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola 34 25 0 09 Oct 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
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 14 23 0 30 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
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 55 134 0 02 May 2023
A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material Mengchun Zhang Maryam Qamar Taegoo Kang Yuna Jung Chenshuang Zhang Sung-Ho Bae Chaoning Zhang DiffM MedIm 31 44 0 04 Apr 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 26 6 0 23 Feb 2023
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action Zhiye Guo Jian Liu Yanli Wang Mengrui Chen Duolin Wang Dong Xu Jianlin Cheng MedIm AI4CE DiffM 46 22 0 13 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications C. Liu Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 32 58 0 06 Feb 2023
Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy Yufei Huang Lirong Wu Haitao Lin Jiangbin Zheng Ge Wang Stan Z. Li DiffM 24 14 0 05 Feb 2023
A Survey on Protein Representation Learning: Retrospect and Prospect Lirong Wu Yu-Feng Huang H. Lin Stan Z. Li AI4TS 26 12 0 31 Dec 2022
Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective Cheng Tan Zhangyang Gao Hanqun Cao Xingran Chen Ge Wang Lirong Wu Jun-Xiong Xia Jiangbin Zheng Stan Z. Li 19 1 0 02 Dec 2022
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 33 194 0 24 Oct 2022
A Survey on Generative Diffusion Model Hanqun Cao Cheng Tan Zhangyang Gao Yilun Xu Guangyong Chen Pheng-Ann Heng Stan Z. Li MedIm 37 206 0 06 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
AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB Zhangyang Gao Cheng Tan Stan Z. Li 144 52 0 01 Feb 2022
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs Zhao Xu Youzhi Luo Xuan Zhang Xinyi Xu Yaochen Xie Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 40 39 0 30 Sep 2021
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 191 633 0 29 Nov 2018