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"

50 / 94 papers shown

Title
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule Keyue Qiu Yuxuan Song Zhehuan Fan Peidong Liu Zhe Zhang Mingyue Zheng Hao Zhou Wei-Ying Ma 31 0 0 12 May 2025
A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization Anjie Qiao Hao Zhang Qianmu Yuan Qirui Deng Jingtian Su Yifan Jiang Huihao Zhou Guo-Bo Li Zhilin 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 Yifan Jiang Hao Zhang Jiahua Rao Shuangjia Zheng Yuedong Yang Zhilin Wang Guo-Bo Li J. Lei DiffM MedIm 38 0 0 29 Apr 2025
AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification Maximilian G. Schuh Joshua Hesse Stephan A. Sieber 25 1 0 15 Apr 2025
FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation Julian Cremer Ross Irwin Alessandro Tibot J. Janet Simon Olsson Djork-Arné Clevert 35 0 0 14 Apr 2025
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
Compositional Flows for 3D Molecule and Synthesis Pathway Co-design Tony Shen Seonghwan Seo Ross Irwin Kieran Didi Simon Olsson Woo Youn Kim Martin Ester 51 0 0 10 Apr 2025
PharmAgents: Building a Virtual Pharma with Large Language Model Agents B. Gao Yanwen Huang Yiqiao Liu Wenxuan Xie Wei-Ying Ma Ya-Qin Zhang Yanyan Lan LLMAG LM&Ro 81 0 0 28 Mar 2025
TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design Xiuyuan Hu Guoqing Liu Can Chen Yang Zhao Hao Zhang Xue Liu 61 2 0 26 Mar 2025
Data augmentation using diffusion models to enhance inverse Ising inference Yechan Lim Sangwon Lee Junghyo Jo DiffM 48 0 0 13 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 48 0 0 11 Mar 2025
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows Xiangxin Zhou Yi Xiao Haowei Lin Xinheng He Jiaqi Guan Yang Wang Qiang Liu F. I. S. Kevin Zhou Liang Wang Jianzhu Ma AI4CE 55 0 0 06 Mar 2025
Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model Bernard Ghanem Chenran Jiang Ziqi Gao Yu Liu Chenyang Liu Jiean Chen Yong Huang Jia Li 46 0 0 02 Mar 2025
Symmetry-Preserving Diffusion Models via Target Symmetrization Vinh Tong Yun Ye Trung-Dung Hoang Anji Liu Guy Van den Broeck Mathias Niepert DiffM 82 0 0 17 Feb 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance Ziqi Chen B. Peng Tianhua Zhai Daniel Adu-Ampratwum Xia Ning 63 1 0 09 Feb 2025
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Ali Khodabandeh Yalabadi Mehdi Yazdani-Jahromi O. Garibay 41 0 0 28 Jan 2025
Score-based 3D molecule generation with neural fields Matthieu Kirchmeyer Pedro H. O. Pinheiro Saeed Saremi DiffM 48 0 0 15 Jan 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 34 0 0 05 Jan 2025
Rectified Flow For Structure Based Drug Design Daiheng Zhang Chengyue Gong Qiang Liu DiffM 82 0 0 02 Dec 2024
Exploring Discrete Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes 92 4 0 25 Nov 2024
ET-SEED: Efficient Trajectory-Level SE(3) Equivariant Diffusion Policy Chenrui Tie Yue Chen Ruihai Wu Boxuan Dong Z. Li Chongkai Gao Hao Dong 51 3 0 06 Nov 2024
Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design Xiangxin Zhou Jiaqi Guan Yunke Zhang Xingang Peng Liang Wang Jianzhu Ma 26 2 0 28 Oct 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
Text-Guided Multi-Property Molecular Optimization with a Diffusion Language Model Yida Xiong Kun Li Weiwei Liu Jia Wu Bo Du Shirui Pan Wenbin Hu 25 1 0 17 Oct 2024
The Latent Road to Atoms: Backmapping Coarse-grained Protein Structures with Latent Diffusion Xu Han Yuancheng Sun Kai Chen Kang Liu Qiwei Ye DiffM AI4CE 24 0 0 17 Oct 2024
Geometric Trajectory Diffusion Models Jiaqi Han Minkai Xu Aaron Lou Haotian Ye Stefano Ermon DiffM 54 4 0 16 Oct 2024
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 42 0 0 15 Oct 2024
GUISE: Graph GaUssIan Shading watErmark Renyi Yang 22 0 0 14 Oct 2024
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules Shikun Feng Yuyan Ni Yan Lu Zhi-Ming Ma Wei-Ying Ma Yanyan Lan 38 5 0 14 Oct 2024
nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder Maksim Kuznetsov Airat Valiev Alex Aliper Daniil Polykovskiy E. Tutubalina Rim Shayakhmetov Z. Miftahutdinov 27 0 0 11 Oct 2024
InstructBioMol: Advancing Biomolecule Understanding and Design Following Human Instructions Xiang Zhuang Keyan Ding Tianwen Lyu Yinuo Jiang Xiaotong Li ... Ming Qin Kehua Feng Jike Wang Qiang Zhang Huajun Chen 33 3 0 10 Oct 2024
Generative Flows on Synthetic Pathway for Drug Design Seonghwan Seo Minsu Kim Tony Shen Martin Ester Jinkyoo Park Sungsoo Ahn Woo Youn Kim 39 3 0 06 Oct 2024
SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design Zygimantas Jocys Henriette M. G. Willems Katayoun Farrahi Katayoun Farrahi 22 0 0 03 Oct 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much? Rafał Karczewski Samuel Kaski Markus Heinonen Vikas K. Garg 33 0 0 12 Aug 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
Equivariant Diffusion Policy Dian Wang Stephen M. Hart David Surovik Tarik Kelestemur Haojie Huang Haibo Zhao Mark Yeatman Jiuguang Wang Robin Walters Robert Platt DiffM 54 21 0 01 Jul 2024
EquiBot: SIM(3)-Equivariant Diffusion Policy for Generalizable and Data Efficient Learning Jingyun Yang Zi-ang Cao Congyue Deng Rika Antonova Shuran Song Jeannette Bohg DiffM 53 29 0 01 Jul 2024
Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization Siyi Gu Minkai Xu Alexander Powers Weili Nie Tomas Geffner Karsten Kreis J. Leskovec Arash Vahdat Stefano Ermon 48 7 0 01 Jul 2024
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design Yue Jian Curtis Wu Danny Reidenbach Aditi S. Krishnapriyan 34 1 0 24 Jun 2024
Geometric-informed GFlowNets for Structure-Based Drug Design Grayson Lee Tony Shen Martin Ester 34 0 0 16 Jun 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
Generative Inverse Design of Crystal Structures via Diffusion Models with Transformers Izumi Takahara Kiyou Shibata Teruyasu Mizoguchi DiffM AI4CE 34 2 0 13 Jun 2024
From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics Bowen Gao Haichuan Tan Yanwen Huang Minsi Ren Xiao Huang Wei-Ying Ma Ya-Qin Zhang Yanyan Lan 35 1 0 13 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 38 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
TAGMol: Target-Aware Gradient-guided Molecule Generation Vineeth Dorna Subhalingam D Keshav Kolluru Shreshth Tuli Mrityunjay Singh Saurabh Singal N. M. A. Krishnan Sayan Ranu 40 2 0 03 Jun 2024
Covariance-Adaptive Sequential Black-box Optimization for Diffusion Targeted Generation Yueming Lyu Kim yong Tan Yew-Soon Ong Ivor W. Tsang DiffM 30 1 0 02 Jun 2024
Regressor-free Molecule Generation to Support Drug Response Prediction Kun Li Xiuwen Gong Shirui Pan Jia Wu Bo Du Wenbin Hu 44 1 0 23 May 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 93 1 0 20 May 2024
Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates Zhenqiao Song Yunlong Zhao Wenxian Shi Wengong Jin Yang Yang Lei Li 29 5 0 13 May 2024