Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

15 May 2022

Papers citing "Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets"

25 / 25 papers shown

Title
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 29 0 0 14 Apr 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
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 40 0 0 15 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 37 3 0 06 Oct 2024
Fragment-Masked Diffusion for Molecular Optimization Kun Li Xiantao Cai Jia Wu Shirui Pan Huiting Xu Bo Du Wenbin Hu 33 0 0 17 Aug 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 43 7 0 01 Jul 2024
Molecular Diffusion Models with Virtual Receptors Matan Halfon Eyal Rozenberg Ehud Rivlin Daniel Freedman 45 0 0 26 Jun 2024
Geometric-informed GFlowNets for Structure-Based Drug Design Grayson Lee Tony Shen Martin Ester 27 0 0 16 Jun 2024
Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate? Kangyu Zheng Yingzhou Lu Zaixi Zhang Zhongwei Wan Yao Ma Marinka Zitnik Tianfan Fu ELM 32 6 0 04 Jun 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 85 0 0 20 May 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 34 20 0 01 Mar 2024
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 20 13 0 02 Jun 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 25 34 0 22 May 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 21 6 0 23 Feb 2023
A Survey on Protein Representation Learning: Retrospect and Prospect Lirong Wu Yu-Feng Huang H. Lin Stan Z. Li AI4TS 20 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 16 60 0 21 Nov 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lió Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 31 193 0 24 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 34 25 0 06 Oct 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 224 1,300 0 02 Sep 2022
Evaluating Self-Supervised Learning for Molecular Graph Embeddings Hanchen Wang Jean Kaddour Shengchao Liu Jian Tang Joan Lasenby Qi Liu 22 20 0 16 Jun 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 65 178 0 20 Mar 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 112 302 0 07 Oct 2021
Vector Neurons: A General Framework for SO(3)-Equivariant Networks Congyue Deng Or Litany Yueqi Duan A. Poulenard Andrea Tagliasacchi Leonidas J. Guibas 3DPC 104 315 0 25 Apr 2021
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models Daniil Polykovskiy Alexander Zhebrak Benjamín Sánchez-Lengeling Sergey Golovanov Oktai Tatanov ... Simon Johansson Hongming Chen Sergey I. Nikolenko Alán Aspuru-Guzik Alex Zhavoronkov ELM 172 633 0 29 Nov 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 219 1,337 0 12 Feb 2018