GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles

8 June 2021

Papers citing "GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles"

50 / 79 papers shown

Title
EDBench: Large-Scale Electron Density Data for Molecular Modeling Hongxin Xiang Ke Li M. Liu Zhixiang Cheng Bin Yao Wenjie Du Jun-Xiong Xia Li Zeng Xin Jin Xiangxiang Zeng 11 0 0 14 May 2025
Adjoint Sampling: Highly Scalable Diffusion Samplers via Adjoint Matching Aaron J. Havens Benjamin Kurt Miller Bing Yan Carles Domingo-Enrich Anuroop Sriram ... Brandon Amos Brian Karrer Xiang Fu Guan-Horng Liu Ricky T. Q. Chen DiffM 50 0 0 16 Apr 2025
PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Models Fanmeng Wang Wentao Guo Qi Ou Hongshuai Wang Haitao Lin Hongteng Xu Zhifeng Gao AI4CE 30 1 0 11 Apr 2025
UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion Gongbo Zhang Y. Li Renqian Luo Pipi Hu Zeru Zhao ... Maik Riechert Li-ming Yuan Lei Chen Haiguang Liu Tao Qin DiffM 46 0 0 09 Mar 2025
Periodic Materials Generation using Text-Guided Joint Diffusion Model Kishalay Das Subhojyoti Khastagir Pawan Goyal Seung-Cheol Lee S. Bhattacharjee Niloy Ganguly DiffM 34 0 0 01 Mar 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
EquiFlow: Equivariant Conditional Flow Matching with Optimal Transport for 3D Molecular Conformation Prediction Qingwen Tian Yuxin Xu Yixuan Yang Zhen Wang Ziqi Liu Pengju Yan Xiaolin Li 74 0 0 15 Dec 2024
Conformation Generation using Transformer Flows Sohil Shah V. Koltun MedIm AI4CE 31 0 0 16 Nov 2024
Integrating Graph Neural Networks and Many-Body Expansion Theory for Potential Energy Surfaces Siqi Chen Zhiqiang Wang Xianqi Deng Yili Shen C. Ju ... Lin Xiong Guo Ling Dieaa Alhmoud Hui Guan Zhou Lin 29 0 0 03 Nov 2024
ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation Majdi Hassan Nikhil Shenoy Jungyoon Lee Hannes Stärk Stephan Thaler Dominique Beaini 27 6 0 29 Oct 2024
Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation Jiwoong Park Yang Shen DiffM 29 0 0 26 Oct 2024
Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning Yuxuan Ren Dihan Zheng Chang-Shu Liu Peiran Jin Yu Shi Lin Huang Jiyan He Shengjie Luo Tao Qin Tie-Yan Liu AI4CE 30 1 0 14 Oct 2024
Efficient Generation of Molecular Clusters with Dual-Scale Equivariant Flow Matching Akshay Subramanian Shuhui Qu Cheol Woo Park Sulin Liu Janghwan Lee Rafael Gómez-Bombarelli 13 0 0 10 Oct 2024
REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring Taewon Kim Hyunjin Seo Sungsoo Ahn Eunho Yang AI4CE 32 1 0 04 Oct 2024
Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations Sijia Wang Chen Wang Zhenhao Zhao Jiqiang Zhang Weiran Cai 21 0 0 21 Sep 2024
Geometry Informed Tokenization of Molecules for Language Model Generation Xiner Li Limei Wang Youzhi Luo Carl N. Edwards Shurui Gui Yuchao Lin Heng Ji Shuiwang Ji 29 6 0 19 Aug 2024
SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning Jiying Zhang Zijing Liu Yu Wang Yu Li DiffM 39 1 0 09 May 2024
Molecular relaxation by reverse diffusion with time step prediction Khaled Kahouli Stefaan S. P. Hessmann Klaus-Robert Muller Shinichi Nakajima Stefan Gugler Niklas W. A. Gebauer DiffM 34 5 0 16 Apr 2024
On Diffusion Process in SE(3)-invariant Space Zihan Zhou Ruiying Liu Jiachen Zheng Xiaoxue Wang Tianshu Yu DiffM 32 1 0 03 Mar 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
Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling Yuwei Yang Siqi Ouyang Xueyu Hu Mingyue Zheng Hao Zhou Lei Li 32 1 0 22 Feb 2024
Generative AI and Process Systems Engineering: The Next Frontier Benjamin Decardi-Nelson Abdulelah S. Alshehri Akshay Ajagekar Fengqi You AI4CE LLMAG 24 24 0 15 Feb 2024
Emerging Opportunities of Using Large Language Models for Translation Between Drug Molecules and Indications David Oniani Jordan Hilsman Chengxi Zang Junmei Wang Lianjin Cai Jan Zawala Yanshan Wang 11 7 0 14 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 19 25 0 13 Feb 2024
Weisfeiler Leman for Euclidean Equivariant Machine Learning Snir Hordan Tal Amir Nadav Dym 44 5 0 04 Feb 2024
Diffusion-Driven Generative Framework for Molecular Conformation Prediction Bobin Yang Jie Deng Zhenghan Chen Ruoxue Wu DiffM 29 0 0 22 Dec 2023
SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction Andac Demir Francis Prael B. Kiziltan 19 2 0 12 Dec 2023
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation Yuyang Wang Ahmed A. A. Elhag Navdeep Jaitly J. Susskind Miguel Angel Bautista DiffM 27 20 0 27 Nov 2023
Multiparameter Persistent Homology for Molecular Property Prediction Andac Demir B. Kiziltan 22 1 0 17 Nov 2023
Gradual Optimization Learning for Conformational Energy Minimization Artem Tsypin L. Ugadiarov Kuzma Khrabrov Alexander Telepov Egor Rumiantsev Alexey Skrynnik Aleksandr I. Panov Dmitry Vetrov E. Tutubalina Artur Kadurin 24 1 0 05 Nov 2023
Investigating the Behavior of Diffusion Models for Accelerating Electronic Structure Calculations D. Rothchild Andrew S. Rosen Eric Taw Connie Robinson Joseph E. Gonzalez Aditi S. Krishnapriyan DiffM 24 2 0 02 Nov 2023
Towards equilibrium molecular conformation generation with GFlowNets Alexandra Volokhova Michal Koziarski Alex Hernández-García Cheng-Hao Liu Santiago Miret Pablo Lemos Luca Thiede Zichao Yan Alán Aspuru-Guzik Yoshua Bengio 26 9 0 20 Oct 2023
Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models Gabriele Corso Yilun Xu Valentin De Bortoli Regina Barzilay Tommi Jaakkola DiffM 19 20 0 19 Oct 2023
Scalable Diffusion for Materials Generation Mengjiao Yang KwangHwan Cho Amil Merchant Pieter Abbeel Dale Schuurmans Igor Mordatch E. D. Cubuk 27 38 0 18 Oct 2023
On Accelerating Diffusion-based Molecular Conformation Generation in SE(3)-invariant Space Zihan Zhou Ruiying Liu Tianshu Yu DiffM 30 0 0 07 Oct 2023
Molecular Conformation Generation via Shifting Scores Zihan Zhou Ruiying Liu Chaolong Ying Ruimao Zhang Tianshu Yu DiffM 29 2 0 12 Sep 2023
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation Sungjun Cho Dae-Woong Jeong Sung Moon Ko Jinwoo Kim Sehui Han Seunghoon Hong Honglak Lee Moontae Lee AI4CE DiffM 30 1 0 08 Sep 2023
ChiENN: Embracing Molecular Chirality with Graph Neural Networks Piotr Gaiñski Michał Koziarski Jacek Tabor Marek Śmieja GNN 32 3 0 05 Jul 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 27 7 0 26 Jun 2023
Augmenting Control over Exploration Space in Molecular Dynamics Simulators to Streamline De Novo Analysis through Generative Control Policies Paloma Gonzalez-Rojas Andrew Emmel L. Martínez Neil Malur G. Rutledge AI4CE 13 0 0 26 Jun 2023
MoleCLUEs: Molecular Conformers Maximally In-Distribution for Predictive Models Michael R. Maser Natasa Tagasovska Jae Hyeon Lee Andrew Watkins 31 0 0 20 Jun 2023
3D molecule generation by denoising voxel grids Pedro H. O. Pinheiro Joshua Rackers J. Kleinhenz Michael R. Maser Omar Mahmood Andrew Watkins Stephen Ra Vishnu Sresht Saeed Saremi DiffM 34 20 0 13 Jun 2023
Von Mises Mixture Distributions for Molecular Conformation Generation K. Swanson Jake Williams Eric Jonas 27 6 0 13 Jun 2023
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction Xuan Lin Lichang Dai Yafang Zhou Zunpeng Yu Wen Zhang ... Li Zeng Hao-Heng Chen Bosheng Song Philip S. Yu Xiangxiang Zeng GNN 21 56 0 08 Jun 2023
Efficient and Equivariant Graph Networks for Predicting Quantum Hamiltonian Haiyang Yu Zhao Xu X. Qian Xiaoning Qian Shuiwang Ji 37 24 0 08 Jun 2023
Manifold Diffusion Fields Ahmed A. A. Elhag Yuyang Wang J. Susskind Miguel Angel Bautista DiffM AI4CE 36 4 0 24 May 2023
3D Molecular Geometry Analysis with 2D Graphs Zhao Xu Yaochen Xie Youzhi Luo Xuan Zhang Xinyi Xu Meng Liu Kaleb Dickerson Cheng Deng Maho Nakata Shuiwang Ji 19 1 0 01 May 2023
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design Zaixin Zhang Qi Liu Cheekong Lee Chang-Yu Hsieh Enhong Chen 15 18 0 12 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 33 0 0 05 Apr 2023
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers Michael R. Maser Ji Won Park J. Lin Jae Hyeon Lee Nathan C. Frey Andrew Watkins 22 5 0 15 Feb 2023