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"

37 / 37 papers shown

Title
ItDPDM: Information-Theoretic Discrete Poisson Diffusion Model Sagnik Bhattacharya Abhiram Gorle Ahmed Mohsin Ahsan Bilal Connor Ding Amit Kumar Singh Yadav Tsachy Weissman DiffM 43 0 0 08 May 2025
IgCraft: A versatile sequence generation framework for antibody discovery and engineering Matthew Greenig Haowen Zhao Vladimir Radenkovic Aubin Ramon Pietro Sormanni 44 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 43 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 129 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 61 15 0 17 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 48 8 0 17 Oct 2024
Free Hunch: Denoiser Covariance Estimation for Diffusion Models Without Extra Costs Severi Rissanen Markus Heinonen Arno Solin DiffM 78 0 0 15 Oct 2024
Convergence of Score-Based Discrete Diffusion Models: A Discrete-Time Analysis Zikun Zhang Zixiang Chen Quanquan Gu DiffM 47 3 0 03 Oct 2024
Unleashing the Denoising Capability of Diffusion Prior for Solving Inverse Problems Jiawei Zhang Jiaxin Zhuang Cheng Jin Gen Li Yuantao Gu DiffM 68 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 66 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 48 5 0 22 May 2024
Divide-and-Conquer Posterior Sampling for Denoising Diffusion Priors Yazid Janati Alain Durmus Eric Moulines Jimmy Olsson DiffM 38 7 0 18 Mar 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
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design Kieran Didi Francisco Vargas Simon V. Mathis Vincent Dutordoir Emile Mathieu U. J. Komorowska Pietro Lió DiffM 30 13 0 14 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 Anji Liu Mathias Niepert Guy Van den Broeck DiffM TPM 19 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 18 6 0 19 Oct 2023
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces Michael S. Jones Kirill Shmilovich Andrew L. Ferguson DiffM 27 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-Xiong Xia Jiangbin Zheng Xihong Yang Yue Liu Bozhen Hu Stan Z. Li 22 14 0 21 Apr 2023
Semi-Equivariant Conditional Normalizing Flows Eyal Rozenberg Daniel Freedman 19 0 0 13 Apr 2023
CamDiff: Camouflage Image Augmentation via Diffusion Model Xuejiao Luo Shuo Wang Zongwei Wu Christos Sakaridis Yun Cheng Deng-Ping Fan Luc Van Gool DiffM 30 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 31 129 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 25 21 0 27 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 16 14 0 05 Feb 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
DiffRF: Rendering-Guided 3D Radiance Field Diffusion Norman Muller Yawar Siddiqui Lorenzo Porzi Samuel Rota Buló Peter Kontschieder Matthias Nießner 27 185 0 02 Dec 2022
DiffusionDet: Diffusion Model for Object Detection Shoufa Chen Pei Sun Yibing Song Ping Luo 37 442 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 35 354 0 14 Nov 2022
Semi-Equivariant Continuous Normalizing Flows for Target-Aware Molecule Generation Eyal Rozenberg Daniel Freedman 11 0 0 09 Nov 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lió Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 24 193 0 24 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 12 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 130 403 0 04 Oct 2022
Protein structure generation via folding diffusion Kevin E. Wu Kevin Kaichuang Yang Rianne van den Berg James Y. Zou Alex X. Lu Ava P. Amini DiffM 25 191 0 30 Sep 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 183 172 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 325 1,584 0 10 Nov 2021
E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials Simon L. Batzner Albert Musaelian Lixin Sun Mario Geiger J. Mailoa M. Kornbluth N. Molinari Tess E. Smidt Boris Kozinsky 190 1,229 0 08 Jan 2021