v1v2 (latest)

Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models

28 October 2021

Papers citing "Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models"

48 / 48 papers shown

Title
FaceLiVT: Face Recognition using Linear Vision Transformer with Structural Reparameterization For Mobile Device Novendra Setyawan Chi-Chia Sun Mao-Hsiu Hsu W. Kuo Jun-Wei Hsieh 119 0 0 12 Jun 2025
A 3D pocket-aware and affinity-guided diffusion model for lead optimization Anjie Qiao Junjie Xie Wenjie Huang Hao Zhang Jiahua Rao Shuangjia Zheng Yuedong Yang Ziyi Wang Guo-Bo Li J. Lei DiffM MedIm 64 0 0 29 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 72 0 0 10 Apr 2025
TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design Xiuyuan Hu Guoqing Liu Can Chen Yang Zhao Hao Zhang Xue Liu 106 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 76 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 91 1 0 06 Mar 2025
Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model Ge Li Chenran Jiang Ziqi Gao Yu Liu Chenyang Liu Jiean Chen Yong Huang Jia Li 76 0 0 02 Mar 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance Ziqi Chen Bo Peng Tianhua Zhai Daniel Adu-Ampratwum Xia Ning 139 1 0 09 Feb 2025
3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery Xiuyuan Hu Guoqing Liu Can Chen Yang Zhao Jun Wang Xue Liu 123 2 0 07 Feb 2025
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Ali Khodabandeh Yalabadi Mehdi Yazdani-Jahromi O. Garibay 112 0 0 28 Jan 2025
Score-based 3D molecule generation with neural fields Matthieu Kirchmeyer Pedro H. O. Pinheiro Saeed Saremi DiffM 121 2 0 15 Jan 2025
Rectified Flow For Structure Based Drug Design Daiheng Zhang Chengyue Gong Qiang Liu DiffM 115 0 0 02 Dec 2024
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models Kiwoong Yoo Owen Oertell Junhyun Lee Sanghoon Lee Jaewoo Kang 73 0 0 28 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 97 3 0 06 Oct 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much? Rafał Karczewski Samuel Kaski Markus Heinonen Vikas Garg 107 0 0 12 Aug 2024
Decomposed Direct Preference Optimization for Structure-Based Drug Design Xiwei Cheng Xiangxin Zhou Yuwei Yang Yu Bao Quanquan Gu 61 3 0 19 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 92 11 0 01 Jul 2024
Molecular Diffusion Models with Virtual Receptors Matan Halfon Eyal Rozenberg Ehud Rivlin Daniel Freedman 87 0 0 26 Jun 2024
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design Yue Jian Curtis Wu Danny Reidenbach Aditi S. Krishnapriyan 74 1 0 24 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 Zhang Yanyan Lan 73 1 0 13 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 105 3 0 03 Jun 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 184 1 0 20 May 2024
Response Matching for generating materials and molecules Bingqing Cheng DiffM 58 1 0 15 May 2024
Structure-based drug design by denoising voxel grids Pedro H. O. Pinheiro Arian R. Jamasb Omar Mahmood Vishnu Sresht Saeed Saremi DiffM 54 9 0 07 May 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes BDL DiffM 95 15 0 30 Apr 2024
DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization Xiangxin Zhou Xiwei Cheng Yuwei Yang Yu Bao Liang Wang Quanquan Gu 89 19 0 07 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 96 75 0 26 Feb 2024
Docking-based generative approaches in the search for new drug candidates Tomasz Danel Jan Leski Sabina Podlewska Igor T. Podolak 66 22 0 22 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 154 0 0 05 Oct 2023
PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling Seonghwan Seo Woo Youn Kim 70 4 0 01 Oct 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 108 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 106 25 0 13 Jun 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 78 37 0 22 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 66 35 0 17 May 2023
Semi-Equivariant Conditional Normalizing Flows Eyal Rozenberg Daniel Freedman 62 0 0 13 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 88 18 0 12 Apr 2023
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 179 162 0 11 Apr 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 101 179 0 06 Mar 2023
PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding Zhangyang Gao Yuqi Hu Cheng Tan Stan Z. Li 115 13 0 14 Feb 2023
3D Molecular Generation via Virtual Dynamics Shuqi Lu Lin Yao X. Chen Hang Zheng Di He Guolin Ke DiffM 61 7 0 12 Feb 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 76 19 0 22 Jan 2023
Structure-based drug discovery with deep learning Rıza Özçelik D. V. Tilborg José Jiménez-Luna F. Grisoni AI4CE 72 38 0 26 Dec 2022
Innovative Drug-like Molecule Generation from Flow-based Generative Model Haotian Zhang Lin Wan 45 0 0 12 Nov 2022
Semi-Equivariant Continuous Normalizing Flows for Target-Aware Molecule Generation Eyal Rozenberg Daniel Freedman 74 0 0 09 Nov 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lio Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 151 227 0 24 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 93 27 0 06 Oct 2022
Graph Neural Networks for Molecules Yuyang Wang Zijie Li A. Farimani GNN AI4CE 152 28 0 12 Sep 2022
Generating 3D Molecules for Target Protein Binding Meng Liu Youzhi Luo Kanji Uchino Koji Maruhashi Shuiwang Ji 78 121 0 19 Apr 2022