SE(3)-Stochastic Flow Matching for Protein Backbone Generation

3 October 2023

Papers citing "SE(3)-Stochastic Flow Matching for Protein Backbone Generation"

50 / 57 papers shown

Title
Clifford Group Equivariant Diffusion Models for 3D Molecular Generation Cong Liu Sharvaree P. Vadgama David Ruhe Erik J Bekkers Patrick Forré DiffM 22 0 0 22 Apr 2025
ProtPainter: Draw or Drag Protein via Topology-guided Diffusion Zhengxi Lu Shizhuo Cheng Yuru Jiang Yan Zhang M. Zhang DiffM 34 0 0 19 Apr 2025
On the minimax optimality of Flow Matching through the connection to kernel density estimation Lea Kunkel Mathias Trabs 34 0 0 17 Apr 2025
An All-Atom Generative Model for Designing Protein Complexes Ruizhe Chen Dongyu Xue Xiangxin Zhou Zaixiang Zheng Xiangxiang Zeng Quanquan Gu 19 0 0 17 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
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows Xiangxin Zhou Yi Xiao Haowei Lin Xinheng He Jiaqi Guan Yang Wang Qiang Liu F. I. S. Kevin Zhou Liang Wang Jianzhu Ma AI4CE 50 0 0 06 Mar 2025
Proteina: Scaling Flow-based Protein Structure Generative Models Tomas Geffner Kieran Didi Zuobai Zhang Danny Reidenbach Zhonglin Cao ... Mario Geiger Christian Dallago E. Küçükbenli Arash Vahdat Karsten Kreis DiffM AI4CE 41 4 0 02 Mar 2025
Learning conformational ensembles of proteins based on backbone geometry Nicolas Wolf Leif Seute Vsevolod Viliuga Simon Wagner Jan Stühmer Frauke Gräter AI4CE 50 0 0 19 Feb 2025
Symmetry-Preserving Diffusion Models via Target Symmetrization Vinh Tong Yun Ye Trung-Dung Hoang Anji Liu Guy Van den Broeck Mathias Niepert DiffM 77 0 0 17 Feb 2025
Learning the Language of Protein Structure Benoit Gaujac Jérémie Donà Liviu Copoiu Timothy Atkinson Thomas Pierrot Thomas D. Barrett 53 10 0 08 Jan 2025
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction Alex Morehead Jianlin Cheng OOD 112 2 0 14 Dec 2024
Fast and Robust Visuomotor Riemannian Flow Matching Policy Haoran Ding Noémie Jaquier Jan Peters Leonel Rozo 86 2 0 14 Dec 2024
Exploring Discrete Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes 92 4 0 25 Nov 2024
ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design Yiming Ma Fei Ye Yi Zhou Zaixiang Zheng Dongyu Xue Quanquan Gu 68 0 0 08 Nov 2024
FoldMark: Protecting Protein Generative Models with Watermarking Zaixi Zhang Ruofan Jin Kaidi Fu Le Cong Marinka Zitnik Mengdi Wang 21 1 0 27 Oct 2024
Training Free Guided Flow Matching with Optimal Control Luran Wang Chaoran Cheng Yizhen Liao Yanru Qu Ge Liu 31 1 0 23 Oct 2024
Efficient Antibody Structure Refinement Using Energy-Guided SE(3) Flow Matching Jiying Zhang Zijing Liu Shengyuan Bai He Cao Yu Li Lei Zhang DiffM 35 1 0 22 Oct 2024
Hessian-Informed Flow Matching Christopher Iliffe Sprague Arne Elofsson Hossein Azizpour 25 0 0 15 Oct 2024
CryoFM: A Flow-based Foundation Model for Cryo-EM Densities Yi Zhou Yilai Li Jing Yuan Quanquan Gu 33 1 0 11 Oct 2024
MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks N. Kim Seongsu Kim Minsu Kim Jinkyoo Park Sungsoo Ahn AI4CE 41 0 0 07 Oct 2024
EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics Chenqing Hua Yong Liu Dinghuai Zhang Odin Zhang Sitao Luan Kevin K. Yang Guy Wolf Doina Precup Shuangjia Zheng 31 5 0 01 Oct 2024
Learning Robotic Manipulation Policies from Point Clouds with Conditional Flow Matching Eugenio Chisari Nick Heppert Max Argus Tim Welschehold Thomas Brox Abhinav Valada 3DPC 50 11 0 11 Sep 2024
ProteinBench: A Holistic Evaluation of Protein Foundation Models Fei Ye Zaixiang Zheng Dongyu Xue Yuning Shen Lihao Wang Yiming Ma Yan Wang X. Wang Xiangxin Zhou Quanquan Gu ELM 40 6 0 10 Sep 2024
ActionFlow: Equivariant, Accurate, and Efficient Policies with Spatially Symmetric Flow Matching Niklas Funk Julen Urain João Carvalho V. Prasad Georgia Chalvatzaki Jan Peters 45 5 0 06 Sep 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 26 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 25 4 0 08 Jul 2024
Reinforcement Learning for Sequence Design Leveraging Protein Language Models Jithendaraa Subramanian Shivakanth Sujit Niloy Irtisam Umong Sain Derek Nowrouzezahrai Samira Ebrahimi Kahou Riashat Islam 36 0 0 03 Jul 2024
FlowMM: Generating Materials with Riemannian Flow Matching Benjamin Kurt Miller Ricky T. Q. Chen Anuroop Sriram Brandon M. Wood 29 32 0 07 Jun 2024
Full-Atom Peptide Design based on Multi-modal Flow Matching Jiahan Li Chaoran Cheng Zuofan Wu Ruihan Guo Shitong Luo Zhizhou Ren Jian-wei Peng Jianzhu Ma 40 15 0 02 Jun 2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules Trevor Norton Debswapna Bhattacharya MedIm DiffM 45 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 26 0 30 May 2024
RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching Divya Nori Wengong Jin AI4CE 42 8 0 29 May 2024
Categorical Flow Matching on Statistical Manifolds Chaoran Cheng Jiahan Li Jian-wei Peng Ge Liu 58 10 0 26 May 2024
Trivialized Momentum Facilitates Diffusion Generative Modeling on Lie Groups Yuchen Zhu Tianrong Chen Lingkai Kong Evangelos A. Theodorou Molei Tao DiffM 35 4 0 25 May 2024
Fisher Flow Matching for Generative Modeling over Discrete Data Oscar Davis Samuel Kessler Mircea Petrache .Ismail .Ilkan Ceylan Michael M. Bronstein A. Bose 40 16 0 23 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
Riemannian Flow Matching Policy for Robot Motion Learning Max Braun Noémie Jaquier Leonel Rozo Tamim Asfour 36 11 0 15 Mar 2024
PPFlow: Target-aware Peptide Design with Torsional Flow Matching Haitao Lin Odin Zhang Huifeng Zhao Dejun Jiang Lirong Wu Zicheng Liu Yufei Huang Stan Z. Li 49 12 0 05 Mar 2024
Extended Flow Matching: a Method of Conditional Generation with Generalized Continuity Equation Noboru Isobe Masanori Koyama Jinzhe Zhang Kohei Hayashi Kenji Fukumizu 37 10 0 29 Feb 2024
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations Jiarui Lu Zuobai Zhang Bozitao Zhong Chence Shi Jian Tang AI4CE 33 1 0 16 Feb 2024
Iterated Denoising Energy Matching for Sampling from Boltzmann Densities Tara Akhound-Sadegh Jarrid Rector-Brooks A. Bose Sarthak Mittal Pablo Lemos ... Siamak Ravanbakhsh Gauthier Gidel Yoshua Bengio Nikolay Malkin Alexander Tong DiffM 37 41 0 09 Feb 2024
Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stärk Bowen Jing Chenyu Wang Gabriele Corso Bonnie Berger Regina Barzilay Tommi Jaakkola BDL 44 45 0 08 Feb 2024
Stable Autonomous Flow Matching Christopher Iliffe Sprague Arne Elofsson Hossein Azizpour 41 1 0 08 Feb 2024
AlphaFold Meets Flow Matching for Generating Protein Ensembles Bowen Jing Bonnie Berger Tommi Jaakkola AI4CE 16 92 0 07 Feb 2024
Equivariant Manifold Neural ODEs and Differential Invariants Emma Andersdotter Fredrik Ohlsson 26 0 0 25 Jan 2024
Improved motif-scaffolding with SE(3) flow matching Jason Yim Andrew Campbell Emile Mathieu Andrew Y. K. Foong Michael Gastegger ... Victor Garcia Satorras Bastiaan S. Veeling Frank Noé Regina Barzilay Tommi Jaakkola 21 31 0 08 Jan 2024
Generative Modeling on Manifolds Through Mixture of Riemannian Diffusion Processes Jaehyeong Jo Sung Ju Hwang DiffM 29 9 0 11 Oct 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
Normalizing flows for lattice gauge theory in arbitrary space-time dimension Ryan Abbott M. S. Albergo Aleksandar Botev D. Boyda Kyle Cranmer ... Ali Razavi Danilo Jimenez Rezende F. Romero-López P. Shanahan Julian M. Urban AI4CE 48 31 0 03 May 2023
Multisample Flow Matching: Straightening Flows with Minibatch Couplings Aram-Alexandre Pooladian Heli Ben-Hamu Carles Domingo-Enrich Brandon Amos Y. Lipman Ricky T. Q. Chen 60 126 0 28 Apr 2023