3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery

7 February 2025

Papers citing "3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery"

47 / 47 papers shown

Title
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
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 76 6 0 06 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 70 7 0 04 Jun 2024
Deep Learning for Protein-Ligand Docking: Are We There Yet? Alex Morehead Nabin Giri Jian Liu Jianlin Cheng Jianlin Cheng OOD 105 7 0 23 May 2024
Design Editing for Offline Model-based Optimization Ye Yuan Youyuan Zhang Can Chen Haolun Wu Zixuan Li Jianmo Li James J. Clark Xue Liu 119 5 0 22 May 2024
Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction Eric Alcaide Zhifeng Gao Guolin Ke Yaqi Li Linfeng Zhang Hang Zheng G. Zhou 60 6 0 20 May 2024
Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion Bowen Gao Minsi Ren Yuyan Ni Yanwen Huang Yiran Zhou Zhiming Ma Wei-Ying Ma Yanyan Lan 73 6 0 04 Mar 2024
Deep Confident Steps to New Pockets: Strategies for Docking Generalization Gabriele Corso Arthur Deng Benjamin Fry Nicholas Polizzi Regina Barzilay Tommi Jaakkola OOD 93 34 0 28 Feb 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
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents Xiuyuan Hu Guoqing Liu Yang Zhao Hao Zhang 76 22 0 21 Dec 2023
Protein-ligand binding representation learning from fine-grained interactions Shikun Feng Minghao Li Yinjun Jia Wei-Ying Ma Yanyan Lan SSL AI4CE 68 10 0 09 Nov 2023
FABind: Fast and Accurate Protein-Ligand Binding Qizhi Pei Kaiyuan Gao Lijun Wu Jinhua Zhu Yingce Xia Shufang Xie Tao Qin Kun He Tie-Yan Liu Rui Yan 127 21 0 10 Oct 2023
Drug Discovery with Dynamic Goal-aware Fragments Seul Lee Seanie Lee Kenji Kawaguchi Sung Ju Hwang 102 9 0 02 Oct 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
Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files Daniel Flam-Shepherd Alán Aspuru-Guzik 116 57 0 09 May 2023
Utilizing Reinforcement Learning for de novo Drug Design Hampus Gummesson Svensson C. Tyrchan Ola Engkvist M. Chehreghani 86 20 0 30 Mar 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 101 178 0 06 Mar 2023
Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation? G. Zhou Zhifeng Gao Zhewei Wei Hang Zheng Guolin Ke OOD AI4CE BDL 71 16 0 14 Feb 2023
The Role of AI in Drug Discovery: Challenges, Opportunities, and Strategies Alexandre Blanco-Gonzalez Alfonso Cabezon Alejandro Seco-Gonzalez Daniel Conde-Torres Paula Antelo-Riveiro Ángel Piñeiro R. García‐Fandiño 51 281 0 08 Dec 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 104 55 0 28 Nov 2022
A Systematic Survey of Chemical Pre-trained Models Jun Xia Yanqiao Zhu Yuanqi Du Stan Z.Li AI4CE 138 53 0 29 Oct 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
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 95 110 0 19 Oct 2022
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 260 447 0 04 Oct 2022
Unified 2D and 3D Pre-Training of Molecular Representations Jinhua Zhu Yingce Xia Lijun Wu Shufang Xie Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 106 71 0 14 Jul 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 99 49 0 17 Jun 2022
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets Xingang Peng Shitong Luo Jiaqi Guan Qi Xie Jian-wei Peng Jianzhu Ma 98 190 0 15 May 2022
Generating 3D Molecules for Target Protein Binding Meng Liu Youzhi Luo Kanji Uchino Koji Maruhashi Shuiwang Ji 78 121 0 19 Apr 2022
Structure-aware Protein Self-supervised Learning Can Chen Jingbo Zhou Fan Wang Xue Liu Dejing Dou SSL 93 69 0 06 Apr 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 185 90 0 28 Mar 2022
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 168 186 0 20 Mar 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 110 270 0 07 Feb 2022
Deep Molecular Representation Learning via Fusing Physical and Chemical Information Shuwen Yang Ziyao Li Guojie Song Lingsheng Cai AI4CE 99 31 0 28 Nov 2021
Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models Matthew Ragoza Tomohide Masuda D. Koes DiffM 69 117 0 28 Oct 2021
Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation Soojung Yang Doyeong Hwang Seul Lee Seongok Ryu Sung Ju Hwang 115 73 0 04 Oct 2021
Motif-based Graph Self-Supervised Learning for Molecular Property Prediction Zaixin Zhang Qi Liu Hao Wang Chengqiang Lu Chee-Kong Lee SSL AI4CE 101 259 0 03 Oct 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 142 308 0 26 Jul 2021
Property-Aware Relation Networks for Few-Shot Molecular Property Prediction Yaqing Wang Abulikemu Abuduweili Quanming Yao Dejing Dou 93 70 0 16 Jul 2021
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction Xiaomin Fang Lihang Liu Jieqiong Lei Donglong He Shanzhuo Zhang Jingbo Zhou Fan Wang Hua Wu Haifeng Wang AI4CE 71 458 0 11 Jun 2021
Guiding Deep Molecular Optimization with Genetic Exploration SungSoo Ahn Junsup Kim Hankook Lee Jinwoo Shin 100 76 0 04 Jul 2020
Language Models are Few-Shot Learners Tom B. Brown Benjamin Mann Nick Ryder Melanie Subbiah Jared Kaplan ... Christopher Berner Sam McCandlish Alec Radford Ilya Sutskever Dario Amodei BDL 957 42,622 0 28 May 2020
Reinforcement Learning for Molecular Design Guided by Quantum Mechanics G. Simm Robert Pinsler José Miguel Hernández-Lobato AI4CE 89 85 0 18 Feb 2020
Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction P. Schwaller Teodoro Laino John McGuinness A. Horváth Constantine Bekas A. Lee 115 750 0 06 Nov 2018
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.8K 95,454 0 11 Oct 2018
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 312 905 0 07 Jun 2018
Molecular De Novo Design through Deep Reinforcement Learning Marcus Olivecrona T. Blaschke Ola Engkvist Hongming Chen BDL 156 1,025 0 25 Apr 2017
On Large-Batch Training for Deep Learning: Generalization Gap and Sharp Minima N. Keskar Dheevatsa Mudigere J. Nocedal M. Smelyanskiy P. T. P. Tang ODL 507 2,947 0 15 Sep 2016