Learning to design drug-like molecules in three-dimensional space using deep generative models

17 April 2021

Papers citing "Learning to design drug-like molecules in three-dimensional space using deep generative models"

38 / 38 papers shown

Title
Resource Governance in Networked Systems via Integrated Variational Autoencoders and Reinforcement Learning Qiliang Chen Babak Heydari DRL 32 0 0 30 Oct 2024
Hybrid Generative AI for De Novo Design of Co-Crystals with Enhanced Tabletability Nina Gubina Andrei Dmitrenko Gleb Solovev Lyubov Yamshchikova Oleg Petrov Ivan Lebedev N. Serov Grigorii Kirgizov Nikolay Nikitin Vladimir Vinogradov 23 0 0 22 Oct 2024
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning Jiaqing Xie Yue Zhao 33 0 0 02 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 33 0 0 12 Aug 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 87 1 0 20 May 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 33 10 0 17 Mar 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 27 68 0 26 Feb 2024
FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction Alexander Telepov Artem Tsypin Kuzma Khrabrov Sergey Yakukhnov Pavel Strashnov ... Egor Rumiantsev Daniel Ezhov Manvel Avetisian Olga Popova Artur Kadurin 25 4 0 18 Jan 2024
Binding-Adaptive Diffusion Models for Structure-Based Drug Design Zhilin Huang Ling Yang Zaixi Zhang Xiangxin Zhou Yu Bao Xiawu Zheng Yuwei Yang Yu Wang Wenming Yang DiffM 37 8 0 15 Jan 2024
Autoregressive fragment-based diffusion for pocket-aware ligand design Mahdi Ghorbani Leo Gendelev Paul Beroza Michael J. Keiser DiffM 23 8 0 15 Dec 2023
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 28 45 0 12 Dec 2023
Docking-based generative approaches in the search for new drug candidates Tomasz Danel Jan Leski Sabina Podlewska Igor T. Podolak 19 22 0 22 Nov 2023
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation Gregory W. Kyro Anton Morgunov Rafael I. Brent Victor S. Batista 30 12 0 11 Sep 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
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 31 12 0 17 May 2023
MolDiff: Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation Xingang Peng Jiaqi Guan Qiang Liu Jianzhu Ma DiffM 33 43 0 11 May 2023
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D Bo Qiang Yuxuan Song Minkai Xu Jingjing Gong B. Gao Hao Zhou Weiying Ma Yanyan Lan DiffM 42 18 0 05 May 2023
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 55 134 0 02 May 2023
A Comprehensive Survey on Deep Graph Representation Learning Wei Ju Zheng Fang Yiyang Gu Zequn Liu Qingqing Long ... Jingyang Yuan Yusheng Zhao Yifan Wang Xiao Luo Ming Zhang GNN AI4TS 31 141 0 11 Apr 2023
Beyond Games: A Systematic Review of Neural Monte Carlo Tree Search Applications Marco Kemmerling Daniel Lutticke Robert H. Schmitt 24 14 0 14 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 23 162 0 06 Mar 2023
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow Fangce Sun Zhihao Zhan Hongyu Guo Ming Zhang Jian Tang 26 6 0 23 Feb 2023
Multi-Constraint Molecular Generation using Sparsely Labelled Training Data for Localized High-Concentration Electrolyte Diluent Screening J. Mailoa Xin Li J. Qiu Shengyu Zhang 15 0 0 12 Jan 2023
Protein-Ligand Complex Generator & Drug Screening via Tiered Tensor Transform J. Mailoa Zhaofeng Ye J. Qiu Chang-Yu Hsieh Shengyu Zhang 24 3 0 03 Jan 2023
Structure-based drug discovery with deep learning Rıza Özçelik D. V. Tilborg José Jiménez-Luna F. Grisoni AI4CE 19 35 0 26 Dec 2022
Reinforced Genetic Algorithm for Structure-based Drug Design Tianfan Fu Wenhao Gao Connor W. Coley Jimeng Sun 25 51 0 28 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
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 44 104 0 19 Oct 2022
Artificial Intelligence in Material Engineering: A review on applications of AI in Material Engineering Lipichanda Goswami Manoj Deka Mohendra Roy AI4CE 31 19 0 15 Sep 2022
Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model Yaqin Li Lingli Li Yongjin Xu Yi Yu 17 0 0 14 Aug 2022
PGMG: A Pharmacophore-Guided Deep Learning Approach for Bioactive Molecular Generation Hui Zhu Renyi Zhou Jing Tang Min Li BDL 13 4 0 02 Jul 2022
Cluster Generation via Deep Energy-Based Model A. Y. Artsukevich S. Lepeshkin 21 0 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 25 176 0 15 May 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 25 86 0 28 Mar 2022
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
3DMolNet: A Generative Network for Molecular Structures V. Nesterov Mario Wieser Volker Roth AI4CE 164 33 0 08 Oct 2020
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 179 633 0 29 Nov 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 224 1,337 0 12 Feb 2018