Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models

16 October 2020

Papers citing "Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models"

30 / 30 papers shown

Title
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
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
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
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 33 18 0 18 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 35 10 0 17 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 51 12 0 05 Mar 2024
Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion Bowen Gao Minsi Ren Yuyan Ni Yanwen Huang Bo Qiang Zhiming Ma Wei-Ying Ma Yanyan Lan 34 4 0 04 Mar 2024
Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling Yuwei Yang Siqi Ouyang Xueyu Hu Mingyue Zheng Hao Zhou Lei Li 32 1 0 22 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 29 0 0 28 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 30 45 0 12 Dec 2023
Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods Minsi Ren Bowen Gao Bo Qiang 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 91 0 0 05 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
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 55 135 0 02 May 2023
PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding Zhangyang Gao Yuqi Hu Cheng Tan Stan Z. Li 31 13 0 14 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
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 21 60 0 21 Nov 2022
Innovative Drug-like Molecule Generation from Flow-based Generative Model Haotian Zhang Lin Wan 17 0 0 12 Nov 2022
Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design Kehan Wu Yingce Xia Yang Fan Pan Deng Haiguang Liu Lijun Wu Shufang Xie Tong Wang Tao Qin Tie-Yan Liu 17 2 0 30 Aug 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 27 176 0 15 May 2022
In-Pocket 3D Graphs Enhance Ligand-Target Compatibility in Generative Small-Molecule Creation Seung-gu Kang J. Weber Joseph A. Morrone Leili Zhang T. Huynh Wendy D. Cornell DiffM 13 3 0 05 Apr 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 31 86 0 28 Mar 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
Molecule Generation for Drug Design: a Graph Learning Perspective Nianzu Yang Huaijin Wu Xiaoyong Pan Ye Yuan Junchi Yan 19 13 0 18 Feb 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 22 262 0 07 Feb 2022
De Novo Molecular Generation with Stacked Adversarial Model Yuansan Liu James Bailey GAN BDL 11 1 0 24 Oct 2021
Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models Matthew Ragoza Tomohide Masuda D. Koes DiffM MedIm 67 31 0 17 Oct 2020
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 224 1,338 0 12 Feb 2018