Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem

8 June 2022

Papers citing "Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem"

50 / 51 papers shown

Title
Whitened Score Diffusion: A Structured Prior for Imaging Inverse Problems Jeffrey Alido Tongyu Li Yu Sun Lei Tian DiffM MedIm 19 0 0 15 May 2025
ItDPDM: Information-Theoretic Discrete Poisson Diffusion Model Sagnik Bhattacharya Abhiram Gorle Ahmed Mohsin Ahsan Bilal Connor Ding Amit Kumar Singh Yadav Tsachy Weissman DiffM 45 0 0 08 May 2025
From Missing Pieces to Masterpieces: Image Completion with Context-Adaptive Diffusion Pourya Shamsolmoali Masoumeh Zareapoor Huiyu Zhou Michael Felsberg Dacheng Tao Xuelong Li DiffM 39 0 0 19 Apr 2025
IgCraft: A versatile sequence generation framework for antibody discovery and engineering Matthew Greenig Haowen Zhao Vladimir Radenkovic Aubin Ramon Pietro Sormanni 49 0 0 25 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
Conditional sampling within generative diffusion models Zheng Zhao Ziwei Luo Jens Sjölund Thomas B. Schon DiffM VLM 73 3 0 20 Feb 2025
VipDiff: Towards Coherent and Diverse Video Inpainting via Training-free Denoising Diffusion Models Chaohao Xie Kai Han Kwan-Yee K. Wong VGen DiffM 223 0 0 21 Jan 2025
A General Framework for Inference-time Scaling and Steering of Diffusion Models R. Singhal Zachary Horvitz Ryan Teehan Mengye Ren Zhou Yu Kathleen McKeown Rajesh Ranganath DiffM 66 15 0 17 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
Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design Chenyu Wang Masatoshi Uehara Yichun He Amy Wang Tommaso Biancalani Avantika Lal Tommi Jaakkola Sergey Levine Hanchen Wang Aviv Regev 53 9 0 17 Oct 2024
Free Hunch: Denoiser Covariance Estimation for Diffusion Models Without Extra Costs Severi Rissanen Markus Heinonen Arno Solin DiffM 161 0 0 15 Oct 2024
Convergence of Score-Based Discrete Diffusion Models: A Discrete-Time Analysis Zikun Zhang Zixiang Chen Quanquan Gu DiffM 61 3 0 03 Oct 2024
Step-by-Step Reasoning for Math Problems via Twisted Sequential Monte Carlo Shengyu Feng Xiang Kong Shuang Ma Aonan Zhang Dong Yin Chong-Jun Wang Ruoming Pang Yiming Yang LRM 32 0 0 02 Oct 2024
Unleashing the Denoising Capability of Diffusion Prior for Solving Inverse Problems Jiawei Zhang Jiaxin Zhuang Cheng Jin Gen Li Yuantao Gu DiffM 76 1 0 11 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
Conditioning diffusion models by explicit forward-backward bridging Adrien Corenflos Zheng Zhao Simo Särkkä Jens Sjölund Thomas B. Schon DiffM 58 5 0 22 May 2024
AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusion Adeesh Kolluru John R. Kitchin DiffM 47 4 0 07 May 2024
Divide-and-Conquer Posterior Sampling for Denoising Diffusion Priors Yazid Janati Alain Durmus Eric Moulines Jimmy Olsson DiffM 46 7 0 18 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
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
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design Kieran Didi Francisco Vargas Simon Mathis Vincent Dutordoir Emile Mathieu Urszula Julia Komorowska Pietro Lio DiffM 34 14 0 14 Dec 2023
Diffusion for Natural Image Matting Yihan Hu Yiheng Lin Wei Wang Yao-Min Zhao Yunchao Wei Humphrey Shi 33 7 0 10 Dec 2023
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design Chuanrui Wang Bozitao Zhong Zuobai Zhang Narendra Chaudhary Sanchit Misra Jian Tang 25 5 0 30 Nov 2023
Image Inpainting via Tractable Steering of Diffusion Models Guy Van den Broeck Mathias Niepert Mathias Niepert DiffM TPM 33 16 0 28 Nov 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
Stochastic interpolants with data-dependent couplings M. S. Albergo Mark Goldstein Nicholas M. Boffi Rajesh Ranganath Eric Vanden-Eijnden OT 30 30 0 05 Oct 2023
Nearly $d$ -Linear Convergence Bounds for Diffusion Models via Stochastic Localization Joe Benton Valentin De Bortoli Arnaud Doucet George Deligiannidis DiffM 49 103 0 07 Aug 2023
Crystal Structure Prediction by Joint Equivariant Diffusion Rui Jiao Wen-bing Huang Peijia Lin Jiaqi Han Pin Chen Yutong Lu Yang Liu DiffM 27 61 0 30 Jul 2023
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces Michael S. Jones Kirill Shmilovich Andrew L. Ferguson DiffM 36 12 0 23 Jul 2023
Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer Cheng Tan Zhangyang Gao Lirong Wu Jun Xia Jiangbin Zheng Xihong Yang Yue Liu Bozhen Hu Stan Z. Li 37 14 0 21 Apr 2023
Semi-Equivariant Conditional Normalizing Flows Eyal Rozenberg Daniel Freedman 27 0 0 13 Apr 2023
CamDiff: Camouflage Image Augmentation via Diffusion Model Xuejiao Luo Shuo Wang Zongwei Wu Daniel Gehrig Yun Cheng Deng-Ping Fan Luc Van Gool DiffM 36 19 0 11 Apr 2023
DDP: Diffusion Model for Dense Visual Prediction Yuanfeng Ji Zhe Chen Enze Xie Lanqing Hong Xihui Liu Zhaoqiang Liu Tong Lu Zhenguo Li Ping Luo DiffM VLM 47 130 0 30 Mar 2023
DiffTAD: Temporal Action Detection with Proposal Denoising Diffusion Sauradip Nag Xiatian Zhu Jiankang Deng Yi-Zhe Song Tao Xiang DiffM VGen 43 21 0 27 Mar 2023
Restoration-Degradation Beyond Linear Diffusions: A Non-Asymptotic Analysis For DDIM-Type Samplers Sitan Chen Giannis Daras A. Dimakis DiffM 26 62 0 06 Mar 2023
Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy Yufei Huang Lirong Wu Haitao Lin Jiangbin Zheng Ge Wang Stan Z. Li DiffM 31 14 0 05 Feb 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
DiffRF: Rendering-Guided 3D Radiance Field Diffusion Norman Muller Yawar Siddiqui Lorenzo Porzi Samuel Rota Buló Peter Kontschieder Matthias Nießner 46 185 0 02 Dec 2022
Latent Space Diffusion Models of Cryo-EM Structures Karsten Kreis Tim Dockhorn Zihao Li Ellen D. Zhong DiffM 30 15 0 25 Nov 2022
DiffusionDet: Diffusion Model for Object Detection Shoufa Chen Pei Sun Yibing Song Ping Luo 63 443 0 17 Nov 2022
Diffusion Models for Medical Image Analysis: A Comprehensive Survey A. Kazerouni Ehsan Khodapanah Aghdam Moein Heidari Reza Azad Mohsen Fayyaz I. Hacihaliloglu Dorit Merhof DiffM MedIm 49 358 0 14 Nov 2022
Semi-Equivariant Continuous Normalizing Flows for Target-Aware Molecule Generation Eyal Rozenberg Daniel Freedman 29 0 0 09 Nov 2022
SSD-LM: Semi-autoregressive Simplex-based Diffusion Language Model for Text Generation and Modular Control Xiaochuang Han Sachin Kumar Yulia Tsvetkov 45 79 0 31 Oct 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lio Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 44 196 0 24 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 30 47 0 17 Oct 2022
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 generation via folding diffusion Kevin E. Wu Kevin Kaichuang Yang Rianne van den Berg James Zou Alex X. Lu Ava P. Amini DiffM 35 192 0 30 Sep 2022
Diffusion Models: A Comprehensive Survey of Methods and Applications Ling Yang Zhilong Zhang Yingxia Shao Shenda Hong Runsheng Xu Yue Zhao Wentao Zhang Bin Cui Ming-Hsuan Yang DiffM MedIm 224 1,311 0 02 Sep 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 196 173 0 26 May 2022
Palette: Image-to-Image Diffusion Models Chitwan Saharia William Chan Huiwen Chang Chris A. Lee Jonathan Ho Tim Salimans David J. Fleet Mohammad Norouzi DiffM VLM 348 1,593 0 10 Nov 2021