SE(3) diffusion model with application to protein backbone generation

5 February 2023

Papers citing "SE(3) diffusion model with application to protein backbone generation"

34 / 34 papers shown

Title
Flash Invariant Point Attention Andrew Liu Axel Elaldi Nicholas T Franklin Nathan Russell Gurinder S Atwal Yih-En A Ban Olivia Viessmann 4 0 0 16 May 2025
Guide your favorite protein sequence generative model Junhao Xiong Hunter Nisonoff Ishan Gaur Jennifer Listgarten DiffM 56 0 0 07 May 2025
DDPS: Discrete Diffusion Posterior Sampling for Paths in Layered Graphs Hao Luan See-Kiong Ng Chun Kai Ling 54 0 0 29 Apr 2025
Clifford Group Equivariant Diffusion Models for 3D Molecular Generation Cong Liu Sharvaree P. Vadgama David Ruhe Erik Bekkers Patrick Forré DiffM 27 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 41 0 0 19 Apr 2025
All-atom Diffusion Transformers: Unified generative modelling of molecules and materials Chaitanya K. Joshi Xiang Fu Yi-Lun Liao Vahe Gharakhanyan Benjamin Kurt Miller Anuroop Sriram Zachary W. Ulissi DiffM 60 4 0 05 Mar 2025
MotifBench: A standardized protein design benchmark for motif-scaffolding problems Zhuoqi Zheng Bo Zhang Kieran Didi Kevin K. Yang Jason Yim Joseph L. Watson Hai-Feng Chen Brian L. Trippe 54 1 0 20 Feb 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 Modeling on Lie Groups via Euclidean Generalized Score Matching Marco Bertolini Tuan Le Djork-Arné Clevert DiffM 90 0 0 04 Feb 2025
Diffusion Generative Modeling for Spatially Resolved Gene Expression Inference from Histology Images Sichen Zhu Yuchen Zhu Molei Tao Peng-Chao Qiu MedIm 39 1 0 28 Jan 2025
Learning the Language of Protein Structure Benoit Gaujac Jérémie Donà Liviu Copoiu Timothy Atkinson Thomas Pierrot Thomas D. Barrett 69 10 0 08 Jan 2025
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
Joint Localization and Planning using Diffusion Lukas Lao Beyer S. Karaman 38 0 0 26 Sep 2024
Generating Physical Dynamics under Priors Zihan Zhou Xiaoxue Wang Tianshu Yu DiffM AI4CE 72 0 0 01 Sep 2024
RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design Rishabh Anand Chaitanya K. Joshi Alex Morehead Arian R. Jamasb Charles Harris Simon Mathis Kieran Didi Bryan Hooi Pietro Liò Pietro Liò 58 3 0 19 Jun 2024
Neural Approximate Mirror Maps for Constrained Diffusion Models Berthy Feng Ricardo Baptista Katherine Bouman MedIm DiffM 48 3 0 18 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
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 34 28 0 30 May 2024
Trivialized Momentum Facilitates Diffusion Generative Modeling on Lie Groups Yuchen Zhu Tianrong Chen Lingkai Kong Evangelos A. Theodorou Molei Tao DiffM 40 5 0 25 May 2024
AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusion Adeesh Kolluru John R. Kitchin DiffM 47 4 0 07 May 2024
Model-based reinforcement learning for protein backbone design Frederic Renard Cyprien Courtot Alfredo Reichlin Oliver Bent 45 0 0 03 May 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
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 40 41 0 09 Feb 2024
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion Alex Morehead Jeffrey A. Ruffolo Aadyot Bhatnagar Ali Madani DiffM 24 9 0 21 Dec 2023
Denoising Heat-inspired Diffusion with Insulators for Collision Free Motion Planning Junwoo Chang Hyunwoo Ryu Jiwoo Kim Soochul Yoo Jongeun Choi Joohwan Seo N. Prakash R. Horowitz DiffM AI4CE 28 6 0 19 Oct 2023
Scalable Diffusion for Materials Generation Mengjiao Yang KwangHwan Cho Amil Merchant Pieter Abbeel Dale Schuurmans Igor Mordatch E. D. Cubuk 31 39 0 18 Oct 2023
Generative Modeling on Manifolds Through Mixture of Riemannian Diffusion Processes Jaehyeong Jo Sung Ju Hwang DiffM 39 9 0 11 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
SE(3) Equivariant Augmented Coupling Flows Laurence I. Midgley Vincent Stimper Javier Antorán Emile Mathieu Bernhard Schölkopf José Miguel Hernández-Lobato 42 23 0 20 Aug 2023
Confronting Ambiguity in 6D Object Pose Estimation via Score-Based Diffusion on SE(3) Tsu-Ching Hsiao Haoming Chen Hsuan-Kung Yang Chun-Yi Lee DiffM 23 7 0 25 May 2023
Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds Yeqing Lin Mohammed AlQuraishi DiffM AI4CE 27 75 0 29 Jan 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 196 173 0 26 May 2022
Riemannian Score-Based Generative Modelling Valentin De Bortoli Emile Mathieu M. Hutchinson James Thornton Yee Whye Teh Arnaud Doucet DiffM 222 165 0 06 Feb 2022