Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking

15 November 2021

Papers citing "Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking"

50 / 71 papers shown

Title
SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation Fanglei Xue Meihan Zhang Shuqi Li Xinyu Gao James A. Wohlschlegel Wenbing Huang Yi Yang Weixian Deng 71 0 0 26 Feb 2025
Learning the Language of Protein Structure Benoit Gaujac Jérémie Donà Liviu Copoiu Timothy Atkinson Thomas Pierrot Thomas D. Barrett 58 10 0 08 Jan 2025
Unified Guidance for Geometry-Conditioned Molecular Generation Sirine Ayadi Leon Hetzel Johanna Sommer Fabian J. Theis Stephan Günnemann 34 0 0 05 Jan 2025
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
SE(3)-bi-equivariant Transformers for Point Cloud Assembly Ziming Wang Rebecka Jörnsten 3DPC 43 2 0 12 Jul 2024
BiEquiFormer: Bi-Equivariant Representations for Global Point Cloud Registration Stefanos Pertigkiozoglou Evangelos Chatzipantazis Kostas Daniilidis 3DPC 43 1 0 11 Jul 2024
Generative Model for Small Molecules with Latent Space RL Fine-Tuning to Protein Targets Ulrich A. Mbou Sob Qiulin Li Miguel Arbesú Oliver E. Bent Andries P. Smit Arnu Pretorius 39 1 0 02 Jul 2024
FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames R. Wu Ruihan Guo Rui Wang Shitong Luo Yue Xu Jiahan Li Jianzhu Ma Qiang Liu Yunan Luo Jian Peng 34 1 0 01 Jul 2024
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design Yue Jian Curtis Wu Danny Reidenbach Aditi S. Krishnapriyan 34 1 0 24 Jun 2024
Multi-level Interaction Modeling for Protein Mutational Effect Prediction Yuanle Mo Xin Hong Bowen Gao Yinjun Jia Yanyan Lan AI4CE 24 2 0 28 May 2024
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering Yiqing Shen Outongyi Lv Houying Zhu Yu Guang Wang 38 4 0 21 Apr 2024
Revealing data leakage in protein interaction benchmarks Anton Bushuiev Roman Bushuiev Jiri Sedlar Tomáš Pluskal Jiří Damborský Stanislav Mazurenko Josef Sivic 29 3 0 16 Apr 2024
HelixFold-Multimer: Elevating Protein Complex Structure Prediction to New Heights Xiaomin Fang Jie Gao Jing Hu Lihang Liu Yang Xue Xiaonan Zhang Kunrui Zhu 22 5 0 16 Apr 2024
VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification Florian Sestak Lisa Schneckenreiter Johannes Brandstetter Sepp Hochreiter Andreas Mayr G. Klambauer 31 7 0 10 Apr 2024
PROflow: An iterative refinement model for PROTAC-induced structure prediction Yiran Zhou Wenxian Shi Yuxuan Song Menghua Wu 40 1 0 10 Apr 2024
HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning Rong Han Wenbing Huang Lingxiao Luo Xinyan Han Jiaming Shen Qing Cui Jun Zhou Ting Chen 41 2 0 02 Apr 2024
Equivariant Local Reference Frames for Unsupervised Non-rigid Point Cloud Shape Correspondence Ling Wang Runfa Chen Yikai Wang Gang Hua Xinzhou Wang Sun Kai Guangyuan Fu Jianwei Zhang Wenbing Huang 3DPC 44 1 0 01 Apr 2024
Deep Reinforcement Learning for Modelling Protein Complexes Ziqi Gao Tao Feng Jiaxuan You Chenyi Zi Yan Zhou Chen Zhang Jia Li 48 5 0 11 Mar 2024
SGNet: Folding Symmetrical Protein Complex with Deep Learning Zhaoqun Li Jingcheng Yu Qiwei Ye 23 0 0 07 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
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 40 68 0 26 Feb 2024
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge Yufei Huang Odin Zhang Lirong Wu Cheng Tan Haitao Lin Zhangyang Gao Siyuan Li Stan. Z. Li DiffM 29 6 0 18 Feb 2024
Enhancing Neural Subset Selection: Integrating Background Information into Set Representations Binghui Xie Yatao Bian Kaiwen Zhou Yongqiang Chen Peilin Zhao Bo Han Wei Meng James Cheng 21 1 0 05 Feb 2024
Equivariant Symmetry Breaking Sets YuQing Xie Tess E. Smidt 25 4 0 05 Feb 2024
Fourier Transporter: Bi-Equivariant Robotic Manipulation in 3D Hao-zhe Huang Owen Howell Dian Wang Xu Zhu Robin G. Walters Robert W. Platt 34 22 0 22 Jan 2024
Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction Ziyang Yu Wenbing Huang Yang Liu 19 8 0 17 Jan 2024
xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein Bo Chen Xingyi Cheng Pan Li Yangli-ao Geng Jing Gong ... Chiming Liu Aohan Zeng Yuxiao Dong Jie Tang Leo T. Song 42 101 0 11 Jan 2024
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Ian Dunn D. Koes DiffM GNN 19 3 0 22 Nov 2023
Learning to design protein-protein interactions with enhanced generalization Anton Bushuiev Roman Bushuiev Petr Kouba Anatolii Filkin Marketa Gabrielova ... Jiri Sedlar Tomáš Pluskal Jiří Damborský Stanislav Mazurenko Josef Sivic AI4CE 11 15 0 27 Oct 2023
ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking Yi Yi Xu Wan Yatao Bian Ou-Yang Le Peilin Zhao 21 3 0 12 Oct 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 42 19 0 10 Oct 2023
DockGame: Cooperative Games for Multimeric Rigid Protein Docking Vignesh Ram Somnath Pier Giuseppe Sessa María Rodríguez Martínez Andreas Krause 34 2 0 09 Oct 2023
PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling Seonghwan Seo Woo Youn Kim 18 4 0 01 Oct 2023
Diffusion-EDFs: Bi-equivariant Denoising Generative Modeling on SE(3) for Visual Robotic Manipulation Hyunwoo Ryu Jiwoo Kim Hyun Seok Ahn Junwoo Chang Joohwan Seo Taehan Kim Yubin Kim Chaewon Hwang Jongeun Choi R. Horowitz DiffM 27 33 0 06 Sep 2023
Graph Denoising Diffusion for Inverse Protein Folding Kai Yi Bingxin Zhou Yiqing Shen Pietro Lio' Yu Guang Wang DiffM 11 41 0 29 Jun 2023
Reinforcement Learning-Driven Linker Design via Fast Attention-based Point Cloud Alignment Rebecca M. Neeser Mehmet Akdel Daniel Kovtun Luca Naef 11 6 0 13 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
Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction Jiaxian Yan Zhaofeng Ye Ziyi Yang Chengqiang Lu Shengyu Zhang Qi Liu J. Qiu 35 11 0 08 Jun 2023
AbODE: Ab Initio Antibody Design using Conjoined ODEs Yogesh Verma Markus Heinonen Vikas K. Garg 29 18 0 31 May 2023
SyNDock: N Rigid Protein Docking via Learnable Group Synchronization Yuanfeng Ji Yatao Bian Guoji Fu Peilin Zhao Ping Luo 125 4 0 23 May 2023
Policy Gradient Methods in the Presence of Symmetries and State Abstractions Prakash Panangaden S. Rezaei-Shoshtari Rosie Zhao D. Meger Doina Precup 25 2 0 09 May 2023
Semi-Equivariant Conditional Normalizing Flows Eyal Rozenberg Daniel Freedman 27 0 0 13 Apr 2023
Accurate and Definite Mutational Effect Prediction with Lightweight Equivariant Graph Neural Networks Bingxin Zhou Outongyi Lv Kai Yi Xinye Xiong P. Tan Liang Hong Yu Wang 26 4 0 13 Apr 2023
DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models Mohamed Amine Ketata Cedrik Laue R. Mammadov Hannes Stärk Menghua Wu Gabriele Corso Ćeline Marquet Regina Barzilay Tommi Jaakkola 20 46 0 08 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 35 0 0 05 Apr 2023
Learning Harmonic Molecular Representations on Riemannian Manifold Yiqun Wang Yuning Shen Shih‐Ya Chen Lihao Wang Fei Ye Hao Zhou 43 12 0 27 Mar 2023
Aligned Diffusion Schrödinger Bridges Vignesh Ram Somnath Matteo Pariset Ya-Ping Hsieh María Rodríguez Martínez Andreas Krause Charlotte Bunne DiffM 117 30 0 22 Feb 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 24 5 0 15 Feb 2023
End-to-End Full-Atom Antibody Design Xiangzhe Kong Wenbing Huang Yang Liu 17 48 0 01 Feb 2023
Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equation Wengong Jin Siranush Sarkizova Xun Chen N. Hacohen Caroline Uhler 21 20 0 25 Jan 2023