3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design

15 May 2022

Papers citing "3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design"

37 / 37 papers shown

Title
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 123 23 0 01 Mar 2024
A 3D Generative Model for Structure-Based Drug Design Shitong Luo Jiaqi Guan Jianzhu Ma Jian-wei Peng DiffM 118 185 0 20 Mar 2022
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs Zhao Xu Youzhi Luo Xuan Zhang Xinyi Xu Yaochen Xie Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 63 40 0 30 Sep 2021
An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming Minkai Xu Wujie Wang Shitong Luo Chence Shi Yoshua Bengio Rafael Gómez-Bombarelli Jian Tang 3DV 88 80 0 15 May 2021
Vector Neurons: A General Framework for SO(3)-Equivariant Networks Congyue Deng Or Litany Yueqi Duan A. Poulenard Andrea Tagliasacchi Leonidas Guibas 3DPC 173 325 0 25 Apr 2021
Learning Neural Generative Dynamics for Molecular Conformation Generation Minkai Xu Shitong Luo Yoshua Bengio Jian-wei Peng Jian Tang AI4CE 81 118 0 20 Feb 2021
E(n) Equivariant Graph Neural Networks Victor Garcia Satorras Emiel Hoogeboom Max Welling 108 1,020 0 19 Feb 2021
Equivariant message passing for the prediction of tensorial properties and molecular spectra Kristof T. Schütt Oliver T. Unke M. Gastegger 104 531 0 05 Feb 2021
Symmetry-Aware Actor-Critic for 3D Molecular Design G. Simm Robert Pinsler Gábor Csányi José Miguel Hernández-Lobato AI4CE 68 65 0 25 Nov 2020
Learning from Protein Structure with Geometric Vector Perceptrons Bowen Jing Stephan Eismann Patricia Suriana Raphael J. L. Townshend R. Dror GNN 3DV 67 484 0 03 Sep 2020
SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks F. Fuchs Daniel E. Worrall Volker Fischer Max Welling 3DPC 151 692 0 18 Jun 2020
A Tutorial on VAEs: From Bayes' Rule to Lossless Compression Ronald Yu BDL 33 24 0 18 Jun 2020
Directional Message Passing for Molecular Graphs Johannes Klicpera Janek Groß Stephan Günnemann 122 871 0 06 Mar 2020
Reinforcement Learning for Molecular Design Guided by Quantum Mechanics G. Simm Robert Pinsler José Miguel Hernández-Lobato AI4CE 57 84 0 18 Feb 2020
Decision-Making with Auto-Encoding Variational Bayes Romain Lopez Pierre Boyeau Nir Yosef Michael I. Jordan Jeffrey Regier BDL 390 10,591 0 17 Feb 2020
Hierarchical Generation of Molecular Graphs using Structural Motifs Wengong Jin Regina Barzilay Tommi Jaakkola 69 288 0 08 Feb 2020
GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation Chence Shi Minkai Xu Zhaocheng Zhu Weinan Zhang Ming Zhang Jian Tang 168 437 0 26 Jan 2020
A Generative Model for Molecular Distance Geometry G. Simm José Miguel Hernández-Lobato GAN 75 107 0 25 Sep 2019
Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules Niklas W. A. Gebauer M. Gastegger Kristof T. Schütt 121 208 0 02 Jun 2019
GraphNVP: An Invertible Flow Model for Generating Molecular Graphs Kaushalya Madhawa Katushiko Ishiguro Kosuke Nakago Motoki Abe BDL 100 192 0 28 May 2019
GuacaMol: Benchmarking Models for De Novo Molecular Design Nathan Brown Marco Fiscato Marwin H. S. Segler Alain C. Vaucher ELM 103 707 0 22 Nov 2018
Constrained Generation of Semantically Valid Graphs via Regularizing Variational Autoencoders Tengfei Ma Jie Chen Cao Xiao 118 209 0 07 Sep 2018
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 287 902 0 07 Jun 2018
Constrained Graph Variational Autoencoders for Molecule Design Qi Liu Miltiadis Allamanis Marc Brockschmidt Alexander L. Gaunt BDL 73 455 0 23 May 2018
Learning Deep Generative Models of Graphs Yujia Li Oriol Vinyals Chris Dyer Razvan Pascanu Peter W. Battaglia GNN AI4CE 194 661 0 08 Mar 2018
Syntax-Directed Variational Autoencoder for Structured Data H. Dai Yingtao Tian Bo Dai Steven Skiena Le Song 102 328 0 24 Feb 2018
GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models Jiaxuan You Rex Ying Xiang Ren William L. Hamilton J. Leskovec GNN BDL 116 848 0 24 Feb 2018
Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds Nathaniel Thomas Tess E. Smidt S. Kearnes Lusann Yang Li Li Kai Kohlhoff Patrick F. Riley 3DPC 88 970 0 22 Feb 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 352 1,367 0 12 Feb 2018
GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders M. Simonovsky N. Komodakis GNN BDL 114 849 0 09 Feb 2018
SchNet: A continuous-filter convolutional neural network for modeling quantum interactions Kristof T. Schütt Pieter-Jan Kindermans Huziel Enoc Sauceda Felix Stefan Chmiela A. Tkatchenko K. Müller 155 1,075 0 26 Jun 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 690 131,526 0 12 Jun 2017
Grammar Variational Autoencoder Matt J. Kusner Brooks Paige José Miguel Hernández-Lobato BDL DRL 83 841 0 06 Mar 2017
Automatic chemical design using a data-driven continuous representation of molecules Rafael Gómez-Bombarelli Jennifer N. Wei David Duvenaud José Miguel Hernández-Lobato Benjamín Sánchez-Lengeling Dennis Sheberla J. Aguilera-Iparraguirre Timothy D. Hirzel Ryan P. Adams Alán Aspuru-Guzik 3DV 161 2,929 0 07 Oct 2016
Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering M. Defferrard Xavier Bresson P. Vandergheynst GNN 342 7,650 0 30 Jun 2016
Learning Convolutional Neural Networks for Graphs Mathias Niepert Mohamed Ahmed Konstantin Kutzkov GNN SSL 135 2,154 0 17 May 2016
Gated Graph Sequence Neural Networks Yujia Li Daniel Tarlow Marc Brockschmidt R. Zemel GNN 344 3,282 0 17 Nov 2015