Graph Denoising Diffusion for Inverse Protein Folding

29 June 2023

Yiqing Shen

Papers citing "Graph Denoising Diffusion for Inverse Protein Folding"

31 / 31 papers shown

Title
Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling Xiangxin Zhou Mingyu Li Yi Xiao Jiahan Li Dongyu Xue Zaixiang Zheng Jianzhu Ma Quanquan Gu 5 0 0 27 May 2025
Learning Distributions of Complex Fluid Simulations with Diffusion Graph Networks Mario Lino Tobias Pfaff Nils Thuerey DiffM AI4CE 77 3 0 19 Mar 2025
Backdoor Attacks on Discrete Graph Diffusion Models Jiawen Wang Samin Karim Yuan Hong Binghui Wang DiffM 104 0 0 08 Mar 2025
Mamba-Based Graph Convolutional Networks: Tackling Over-smoothing with Selective State Space Xin He Yansen Wang Wenqi Fan Xu Shen Xin Juan Rui Miao Xin Wang 109 0 0 26 Jan 2025
Quantum Diffusion Model for Quark and Gluon Jet Generation Mariia Baidachna Rey Guadarrama Gopal Ramesh Dahale Tom Magorsch Isabel Pedraza Konstantin T. Matchev Katia Matcheva Kyoungchul Kong S. Gleyzer DiffM 80 0 0 31 Dec 2024
Bridge-IF: Learning Inverse Protein Folding with Markov Bridges Yiheng Zhu Jialu Wu Yue Liu Jiahuan Yan Mingze Yin Wei Wu Mingyang Li Jieping Ye Zehua Wang Jian Wu 48 4 0 04 Nov 2024
E(3)-invariant diffusion model for pocket-aware peptide generation Po-Yu Liang Jun Bai DiffM 23 0 0 27 Oct 2024
Improving Inverse Folding for Peptide Design with Diversity-regularized Direct Preference Optimization Ryan Park Darren J. Hsu C. Brian Roland Maria Korshunova Chen Tessler Shie Mannor Olivia Viessmann Bruno Trentini 42 1 0 25 Oct 2024
Reinforcement learning on structure-conditioned categorical diffusion for protein inverse folding Yasha Ektefaie Olivia Viessmann Siddharth Narayanan Drew Dresser J. Mark Kim Armen Mkrtchyan 44 0 0 22 Oct 2024
DPLM-2: A Multimodal Diffusion Protein Language Model Xinze Wang Zaixiang Zheng Fei Ye Dongyu Xue Shujian Huang Quanquan Gu 33 15 0 17 Oct 2024
How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework Yinuo Ren Haoxuan Chen Grant M. Rotskoff Lexing Ying 54 3 0 04 Oct 2024
TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering Yiqing Shen Zan Chen Michail Mamalakis Yungeng Liu Tianbin Li Yanzhou Su Junjun He Pietro Liò Yu Guang Wang LLMAG 46 9 0 27 Aug 2024
Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion Yutong Hu Y. Tan Andi Han Lirong Zheng Liang Hong Bingxin Zhou DiffM 43 1 0 10 Jul 2024
3D Vessel Graph Generation Using Denoising Diffusion Chinmay Prabhakar Suprosanna Shit Fabio Musio Kaiyuan Yang Tamaz Amiranashvili Johannes C. Paetzold Hongwei Bran Li Bjoern Menze DiffM MedIm 55 3 0 08 Jul 2024
Generative Modelling of Structurally Constrained Graphs Manuel Madeira Clément Vignac D. Thanou Pascal Frossard DiffM 59 3 0 25 Jun 2024
ALPHAGMUT: A Rationale-Guided Alpha Shape Graph Neural Network to Evaluate Mutation Effects Boshen Wang Bowei Ye Lin Xu Jie Liang 34 0 0 13 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 69 17 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 55 2 0 31 May 2024
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering Yiqing Shen Outongyi Lv Houying Zhu Yu Guang Wang 51 4 0 21 Apr 2024
Generative AI for Controllable Protein Sequence Design: A Survey Yiheng Zhu Zitai Kong Jialun Wu Weize Liu Yuqiang Han Mingze Yin Hongxia Xu Chang-Yu Hsieh Tingjun Hou AI4CE 56 6 0 16 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 61 0 0 28 Jan 2024
Fast non-autoregressive inverse folding with discrete diffusion John J. Yang Jason Yim Regina Barzilay Tommi Jaakkola DiffM 13 3 0 05 Dec 2023
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design Chuanrui Wang Bozitao Zhong Zuobai Zhang Narendra Chaudhary Sanchit Misra Jian Tang 30 5 0 30 Nov 2023
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola 65 26 0 09 Oct 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 162 417 0 04 Oct 2022
PiFold: Toward effective and efficient protein inverse folding Zhangyang Gao Cheng Tan Pablo Chacón Stan Z. Li AI4CE 79 104 0 22 Sep 2022
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval Pascal Notin M. Dias J. Frazer Javier Marchena-Hurtado Aidan Gomez D. Marks Y. Gal 62 181 0 27 May 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 199 174 0 26 May 2022
AlphaDesign: A graph protein design method and benchmark on AlphaFoldDB Zhangyang Gao Cheng Tan Stan Z. Li 152 52 0 01 Feb 2022
Diffusion Probabilistic Models for 3D Point Cloud Generation Shitong Luo Wei Hu 3DPC 180 728 0 02 Mar 2021
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions Emiel Hoogeboom Didrik Nielsen P. Jaini Patrick Forré Max Welling DiffM 222 407 0 10 Feb 2021