EigenFold: Generative Protein Structure Prediction with Diffusion Models

5 April 2023

Papers citing "EigenFold: Generative Protein Structure Prediction with Diffusion Models"

36 / 36 papers shown

Title
Topology Guidance: Controlling the Outputs of Generative Models via Vector Field Topology Xiaohan Wang Matthew Berger DiffM 33 0 0 11 May 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
Compositional Flows for 3D Molecule and Synthesis Pathway Co-design Tony Shen Seonghwan Seo Ross Irwin Kieran Didi Simon Olsson Woo Youn Kim Martin Ester 51 0 0 10 Apr 2025
PETIMOT: A Novel Framework for Inferring Protein Motions from Sparse Data Using SE(3)-Equivariant Graph Neural Networks Valentin Lombard Sergei Grudinin É. Laine 29 0 0 19 Mar 2025
Rao-Blackwell Gradient Estimators for Equivariant Denoising Diffusion Vinh Tong Trung-Dung Hoang Anji Liu Guy Van den Broeck Mathias Niepert DiffM 82 0 0 14 Feb 2025
Generative diffusion model with inverse renormalization group flows Kanta Masuki Yuto Ashida DiffM 78 0 0 17 Jan 2025
ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation Majdi Hassan Nikhil Shenoy Jungyoon Lee Hannes Stärk Stephan Thaler Dominique Beaini 29 6 0 29 Oct 2024
Structure Language Models for Protein Conformation Generation Jiarui Lu Xiaoyin Chen Stephen Zhewen Lu Chence Shi Hongyu Guo Yoshua Bengio Xiangbo Shu DiffM 39 2 0 24 Oct 2024
Geometric Trajectory Diffusion Models Jiaqi Han Minkai Xu Aaron Lou Haotian Ye Stefano Ermon DiffM 54 4 0 16 Oct 2024
Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions Xiaoran Jiao Weian Mao Wengong Jin Peiyuan Yang Hao Chen Chunhua Shen 33 0 0 12 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
Loop-Diffusion: an equivariant diffusion model for designing and scoring protein loops Kevin Borisiak Gian Marco Visani Armita Nourmohammad DiffM 29 0 0 26 Sep 2024
ProteinBench: A Holistic Evaluation of Protein Foundation Models Fei Ye Zaixiang Zheng Dongyu Xue Yuning Shen Lihao Wang Yiming Ma Yan Wang Qing Guo Xiangxin Zhou Quanquan Gu ELM 48 6 0 10 Sep 2024
Exploring Selective Layer Fine-Tuning in Federated Learning Yuchang Sun Yuexiang Xie Bolin Ding Yaliang Li Jun Zhang FedML 38 2 0 28 Aug 2024
4D Diffusion for Dynamic Protein Structure Prediction with Reference Guided Motion Alignment Kaihui Cheng Ce Liu Qingkun Su Jun Wang Liwei Zhang Yining Tang Yao Yao Siyu Zhu Yuan Qi DiffM 31 0 0 22 Aug 2024
Improving AlphaFlow for Efficient Protein Ensembles Generation Shaoning Li Mingyu Li Yusong Wang Xinheng He Nanning Zheng Jian Zhang Pheng-Ann Heng 33 4 0 08 Jul 2024
Transferable Boltzmann Generators Leon Klein Frank Noé 49 12 0 20 Jun 2024
Solving Inverse Problems in Protein Space Using Diffusion-Based Priors A. Levy E. R. Chan Sara Fridovich-Keil Frédéric Poitevin Ellen D. Zhong Gordon Wetzstein DiffM 75 3 0 06 Jun 2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules Trevor Norton Debswapna Bhattacharya MedIm DiffM 50 2 0 31 May 2024
Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation Guillaume Huguet James Vuckovic Kilian Fatras Eric Thibodeau-Laufer Pablo Lemos ... Jarrid Rector-Brooks Tara Akhound-Sadegh Michael M. Bronstein Alexander Tong A. Bose 32 28 0 30 May 2024
Protein Conformation Generation via Force-Guided SE(3) Diffusion Models Yan Wang Lihao Wang Yuning Shen Yiqun Wang Huizhuo Yuan Yue Wu Quanquan Gu DiffM 29 25 0 21 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
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations Jiarui Lu Zuobai Zhang Bozitao Zhong Chence Shi Jian Tang AI4CE 44 1 0 16 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 24 26 0 13 Feb 2024
AlphaFold Meets Flow Matching for Generating Protein Ensembles Bowen Jing Bonnie Berger Tommi Jaakkola AI4CE 20 92 0 07 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 32 0 0 28 Jan 2024
Energy based diffusion generator for efficient sampling of Boltzmann distributions Yan Wang Ling Guo Hao Wu Tao Zhou DiffM 36 3 0 04 Jan 2024
Generative artificial intelligence for de novo protein design Adam Winnifrith C. Outeiral Brian L. Hie AI4CE 26 23 0 15 Oct 2023
DockGame: Cooperative Games for Multimeric Rigid Protein Docking Vignesh Ram Somnath Pier Giuseppe Sessa María Rodríguez Martínez Andreas Krause 37 2 0 09 Oct 2023
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola 42 25 0 09 Oct 2023
AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies Karolis Martinkus J. Ludwiczak Kyunghyun Cho Weishao Lian J. Lafrance-Vanasse ... A. Rajpal Yongpeng Wu Richard Bonneau Vladimir Gligorijević Andreas Loukas DiffM 34 37 0 28 Jul 2023
Geometric Constraints in Probabilistic Manifolds: A Bridge from Molecular Dynamics to Structured Diffusion Processes Justin S. Diamond M. Lill DiffM AI4CE 11 1 0 10 Jul 2023
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling Jiarui Lu Bozitao Zhong Zuobai Zhang Jian Tang 19 24 0 05 Jun 2023
Extracting Reward Functions from Diffusion Models Felipe Nuti Tim Franzmeyer João F. Henriques 19 14 0 01 Jun 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 142 412 0 04 Oct 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 190 173 0 26 May 2022