Protein Sequence and Structure Co-Design with Equivariant Translation

17 October 2022

Jian Tang

Papers citing "Protein Sequence and Structure Co-Design with Equivariant Translation"

30 / 30 papers shown

Title
An All-Atom Generative Model for Designing Protein Complexes Ruizhe Chen Dongyu Xue Xiangxin Zhou Zaixiang Zheng Xiangxiang Zeng Quanquan Gu 19 0 0 17 Apr 2025
dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen Cheng Tan Yijie Zhang Zhangyang Gao Yufei Huang Haitao Lin Lirong Wu Fandi Wu Mathieu Blanchette Stan Z. Li AI4CE 46 0 0 01 Mar 2025
A Model-Centric Review of Deep Learning for Protein Design Gregory W. Kyro Tianyin Qiu Victor S. Batista 3DV ELM 65 1 0 26 Feb 2025
A Periodic Bayesian Flow for Material Generation Hanlin Wu Yuxuan Song Jingjing Gong Ziyao Cao Y. Ouyang Jianbing Zhang Hao Zhou Wei-Ying Ma Jingjing Liu DiffM 69 2 0 04 Feb 2025
DPLM-2: A Multimodal Diffusion Protein Language Model Qing Guo Zaixiang Zheng Fei Ye Dongyu Xue Shujian Huang Quanquan Gu 28 13 0 17 Oct 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much? Rafał Karczewski Samuel Kaski Markus Heinonen Vikas K. Garg 33 0 0 12 Aug 2024
Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates Zhenqiao Song Yunlong Zhao Wenxian Shi Wengong Jin Yang Yang Lei Li 29 5 0 13 May 2024
Functional Protein Design with Local Domain Alignment Chaohao Yuan Songyou Li Geyan Ye Yikun Zhang Long-Kai Huang Wenbing Huang Wei Liu Jianhua Yao Yu Rong 29 2 0 18 Apr 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 34 20 0 01 Mar 2024
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations Jiarui Lu Zuobai Zhang Bozitao Zhong Chence Shi Jian Tang AI4CE 38 1 0 16 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 24 25 0 13 Feb 2024
FoldToken: Learning Protein Language via Vector Quantization and Beyond Zhangyang Gao Cheng Tan Jue Wang Yufei Huang Lirong Wu Stan Z. Li 30 9 0 04 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 29 0 0 28 Jan 2024
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation Yongkang Wang Xuan Liu Feng Huang Zhankun Xiong Wen Zhang 57 14 0 25 Dec 2023
Equivariant Flow Matching with Hybrid Probability Transport Yuxuan Song Jingjing Gong Minkai Xu Ziyao Cao Yanyan Lan Stefano Ermon Hao Zhou Wei-Ying Ma DiffM 33 45 0 12 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
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design Fang Wu Stan Z. Li 33 17 0 30 Oct 2023
Equivariant Map and Agent Geometry for Autonomous Driving Motion Prediction Yuping Wang Jier Chen 26 3 0 21 Oct 2023
Functional Geometry Guided Protein Sequence and Backbone Structure Co-Design Justin Dumouchelle Yunlong Zhao Wenxian Shi Yang Yang Lei Li 26 2 0 06 Oct 2023
Joint Design of Protein Sequence and Structure based on Motifs Zhenqiao Song Yunlong Zhao Yufei Song Wenxian Shi Yang Yang Lei Li 3DV DiffM 35 3 0 04 Oct 2023
AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies Karolis Martinkus J. Ludwiczak Kyunghyun Cho Weishao Lian J. Lafrance-Vanasse ... A. Rajpal Yongpeng Wu Richard Bonneau Vladimir Gligorijević Andreas Loukas DiffM 34 37 0 28 Jul 2023
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling Jiarui Lu Bozitao Zhong Zuobai Zhang Jian Tang 19 24 0 05 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 22 13 0 02 Jun 2023
AbODE: Ab Initio Antibody Design using Conjoined ODEs Yogesh Verma Markus Heinonen Vikas K. Garg 29 18 0 31 May 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 18 31 0 06 May 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 34 14 0 21 Apr 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 50 50 0 17 Feb 2023
A Survey on Generative Diffusion Model Hanqun Cao Cheng Tan Zhangyang Gao Yilun Xu Guangyong Chen Pheng-Ann Heng Stan Z. Li MedIm 37 206 0 06 Sep 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 187 173 0 26 May 2022
Diffusion Probabilistic Models for 3D Point Cloud Generation Shitong Luo Wei Hu 3DPC 180 721 0 02 Mar 2021