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"

29 / 29 papers shown

Title
Guide your favorite protein sequence generative model Junhao Xiong Hunter Nisonoff Ishan Gaur Jennifer Listgarten DiffM 51 0 0 07 May 2025
DDPS: Discrete Diffusion Posterior Sampling for Paths in Layered Graphs Hao Luan See-Kiong Ng Chun Kai Ling 52 0 0 29 Apr 2025
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
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 53 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 49 1 0 20 Feb 2025
Diffusion Generative Modeling for Spatially Resolved Gene Expression Inference from Histology Images Sichen Zhu Yuchen Zhu Molei Tao Peng-Chao Qiu MedIm 31 0 0 28 Jan 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
MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks N. Kim Seongsu Kim Minsu Kim Jinkyoo Park Sungsoo Ahn AI4CE 35 0 0 07 Oct 2024
Joint Localization and Planning using Diffusion Lukas Lao Beyer S. Karaman 33 0 0 26 Sep 2024
Generating Physical Dynamics under Priors Zihan Zhou Xiaoxue Wang Tianshu Yu DiffM AI4CE 52 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 V. Mathis Kieran Didi Bryan Hooi Pietro Liò Pietro Liò 50 2 0 19 Jun 2024
Neural Approximate Mirror Maps for Constrained Diffusion Models Berthy T. Feng Ricardo Baptista Katherine L. Bouman MedIm DiffM 40 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 73 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 32 26 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 35 4 0 25 May 2024
Model-based reinforcement learning for protein backbone design Frederic Renard Cyprien Courtot Alfredo Reichlin Oliver Bent 41 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 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 34 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 22 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 20 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 27 38 0 18 Oct 2023
Generative Modeling on Manifolds Through Mixture of Riemannian Diffusion Processes Jaehyeong Jo Sung Ju Hwang DiffM 29 9 0 11 Oct 2023
DockGame: Cooperative Games for Multimeric Rigid Protein Docking Vignesh Ram Somnath Pier Giuseppe Sessa María Rodríguez Martínez Andreas Krause 31 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 30 22 0 20 Aug 2023
Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds Yeqing Lin Mohammed AlQuraishi DiffM AI4CE 12 73 0 29 Jan 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 134 409 0 04 Oct 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 183 173 0 26 May 2022
Riemannian Score-Based Generative Modelling Valentin De Bortoli Emile Mathieu M. Hutchinson James Thornton Yee Whye Teh Arnaud Doucet DiffM 217 164 0 06 Feb 2022