Learning Subpocket Prototypes for Generalizable Structure-based Drug Design

22 May 2023

Qi Liu

Papers citing "Learning Subpocket Prototypes for Generalizable Structure-based Drug Design"

25 / 25 papers shown

Title
TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design Xiuyuan Hu Guoqing Liu Can Chen Yang Zhao Hao Zhang Xue Liu 50 2 0 26 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 50 0 0 06 Mar 2025
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation Ali Khodabandeh Yalabadi Mehdi Yazdani-Jahromi O. Garibay 33 0 0 28 Jan 2025
DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking Jiaxian Yan Zaixi Zhang Jintao Zhu Kai Zhang Jianfeng Pei Qi Liu 21 2 0 15 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 30 0 0 12 Aug 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
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 32 7 0 01 Jul 2024
Geometric-informed GFlowNets for Structure-Based Drug Design Grayson Lee Tony Shen Martin Ester 16 0 0 16 Jun 2024
Graph Sparsification via Mixture of Graphs Guibin Zhang Xiangguo Sun Yanwei Yue Kun Wang Tianlong Chen Shirui Pan 23 8 0 23 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 33 2 0 02 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 27 14 0 07 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 19 4 0 04 Mar 2024
Lo-Hi: Practical ML Drug Discovery Benchmark Simon Steshin VLM 15 7 0 10 Oct 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 84 0 0 05 Oct 2023
Drug Discovery with Dynamic Goal-aware Fragments Seul Lee Seanie Lee Kenji Kawaguchi Sung Ju Hwang 15 5 0 02 Oct 2023
CONVERT:Contrastive Graph Clustering with Reliable Augmentation Xihong Yang Cheng Tan Yue Liu K. Liang Siwei Wang Sihang Zhou Jun-Xiong Xia Stan Z. Li Xinwang Liu En Zhu 30 35 0 17 Aug 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 25 1 0 20 Jun 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 8 13 0 12 Apr 2023
Backdoor Defense via Deconfounded Representation Learning Zaixin Zhang Qi Liu Zhicai Wang Zepu Lu Qingyong Hu AAML 46 39 0 13 Mar 2023
Hierarchical Graph Transformer with Adaptive Node Sampling Zaixin Zhang Qi Liu Qingyong Hu Cheekong Lee 65 82 0 08 Oct 2022
PiFold: Toward effective and efficient protein inverse folding Zhangyang Gao Cheng Tan Pablo Chacón Stan Z. Li AI4CE 59 104 0 22 Sep 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
DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations Yuanfeng Ji Lu Zhang Jiaxiang Wu Bing Wu Long-Kai Huang ... Ping Luo Shuigeng Zhou Junzhou Huang Peilin Zhao Yatao Bian OOD 58 73 0 24 Jan 2022
Vector Neurons: A General Framework for SO(3)-Equivariant Networks Congyue Deng Or Litany Yueqi Duan A. Poulenard Andrea Tagliasacchi Leonidas J. Guibas 3DPC 102 314 0 25 Apr 2021
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 211 1,329 0 12 Feb 2018