MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation

11 May 2023

Papers citing "MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation"

34 / 34 papers shown

Title
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule Keyue Qiu Yuxuan Song Zhehuan Fan Peidong Liu Z. Zhang Mingyue Zheng Hao Zhou Wei-Ying Ma 21 0 0 12 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
Straight-Line Diffusion Model for Efficient 3D Molecular Generation Yuyan Ni Shikun Feng Haohan Chi Bowen Zheng Huan-ang Gao Wei-Ying Ma Zhi-Ming Ma Yanyan Lan DiffM 68 2 0 04 Mar 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance Ziqi Chen B. Peng Tianhua Zhai Daniel Adu-Ampratwum Xia Ning 58 1 0 09 Feb 2025
Score-based 3D molecule generation with neural fields Matthieu Kirchmeyer Pedro H. O. Pinheiro Saeed Saremi DiffM 43 0 0 15 Jan 2025
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models Kiwoong Yoo Owen Oertell Junhyun Lee Sanghoon Lee Jaewoo Kang 31 0 0 28 Oct 2024
Decomposed Direct Preference Optimization for Structure-Based Drug Design Xiwei Cheng Xiangxin Zhou Yuwei Yang Yu Bao Quanquan Gu 36 3 0 19 Jul 2024
3D Vessel Graph Generation Using Denoising Diffusion Chinmay Prabhakar Suprosanna Shit Fabio Musio Kaiyuan Yang Tamaz Amiranashvili Johannes C. Paetzold Hongwei Bran Li Bjoern H. Menze DiffM MedIm 47 2 0 08 Jul 2024
Generative Inverse Design of Crystal Structures via Diffusion Models with Transformers Izumi Takahara Kiyou Shibata Teruyasu Mizoguchi DiffM AI4CE 29 2 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 34 11 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 35 3 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 30 2 0 03 Jun 2024
Regressor-free Molecule Generation to Support Drug Response Prediction Kun Li Xiuwen Gong Shirui Pan Jia Wu Bo Du Wenbin Hu 29 1 0 23 May 2024
Response Matching for generating materials and molecules Bingqing Cheng DiffM 27 1 0 15 May 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes BDL DiffM 44 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 33 18 0 18 Apr 2024
Molecular relaxation by reverse diffusion with time step prediction Khaled Kahouli Stefaan S. P. Hessmann Klaus-Robert Muller Shinichi Nakajima Stefan Gugler Niklas W. A. Gebauer DiffM 34 5 0 16 Apr 2024
Diffusion-Driven Domain Adaptation for Generating 3D Molecules Haokai Hong Wanyu Lin Kay Chen Tan DiffM 34 2 0 01 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 25 10 0 17 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 32 20 0 01 Mar 2024
STRIDE: Structure-guided Generation for Inverse Design of Molecules Shehtab Zaman D. Akhiyarov Mauricio Araya-Polo Kenneth Chiu 13 1 0 06 Nov 2023
AlignDiff: Aligning Diverse Human Preferences via Behavior-Customisable Diffusion Model Zibin Dong Yifu Yuan Jianye Hao Fei Ni Yao Mu Yan Zheng Yujing Hu Tangjie Lv Changjie Fan Zhipeng Hu 34 29 0 03 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 24 0 29 Sep 2023
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models Ziqi Chen B. Peng Srinivas Parthasarathy Xia Ning DiffM 29 5 0 23 Aug 2023
On the Design Fundamentals of Diffusion Models: A Survey Ziyi Chang G. Koulieris Hubert P. H. Shum DiffM 27 50 0 07 Jun 2023
MUDiff: Unified Diffusion for Complete Molecule Generation Chenqing Hua Sitao Luan Minkai Xu Rex Ying Jie Fu Stefano Ermon Doina Precup DiffM 41 34 0 28 Apr 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 13 18 0 12 Apr 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 35 49 0 17 Feb 2023
Diffusion Models for Graphs Benefit From Discrete State Spaces K. Haefeli Karolis Martinkus Nathanael Perraudin Roger Wattenhofer DiffM 77 51 0 04 Oct 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 65 176 0 20 Mar 2022
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions Emiel Hoogeboom Didrik Nielsen P. Jaini Patrick Forré Max Welling DiffM 202 392 0 10 Feb 2021
Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models Matthew Ragoza Tomohide Masuda D. Koes DiffM MedIm 65 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 184 878 0 07 Jun 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 219 1,329 0 12 Feb 2018