End-to-End Full-Atom Antibody Design

1 February 2023

Yang Liu

Papers citing "End-to-End Full-Atom Antibody Design"

24 / 24 papers shown

Title
AbFlowNet: Optimizing Antibody-Antigen Binding Energy via Diffusion-GFlowNet Fusion Abrar Rahman Abir Haz Sameen Shahgir Md Rownok Zahan Ratul Md Toki Tahmid Greg Ver Steeg Yue Dong 7 0 0 18 May 2025
An All-Atom Generative Model for Designing Protein Complexes Ruizhe Chen Dongyu Xue Xiangxin Zhou Zaixiang Zheng Xiangxiang Zeng Quanquan Gu 26 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 48 0 0 01 Mar 2025
Fast and Accurate Antibody Sequence Design via Structure Retrieval Xingyi Zhang Kun Xie Ningqiao Huang Wei Liu Peilin Zhao Sibo Wang Kangfei Zhao Biaobin Jiang 46 0 0 11 Feb 2025
Towards More Accurate Full-Atom Antibody Co-Design Jiayang Wu Xingyi Zhang Xiangyu Dong Kun Xie Ziqi Liu Wensheng Gan Sibo Wang Le Song 49 0 0 11 Feb 2025
Decoupled Sequence and Structure Generation for Realistic Antibody Design Nayoung Kim Minsu Kim Sungsoo Ahn Jinkyoo Park 54 0 0 20 Jan 2025
AlignAb: Pareto-Optimal Energy Alignment for Designing Nature-Like Antibodies Yibo Wen Chenwei Xu Jerry Yao-Chieh Hu Han-Wen Liu DiffM 45 3 0 31 Dec 2024
MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction Cheng Tan Zhenxiao Cao Zhangyang Gao Lirong Wu Siyuan Li Yufei Huang Jun Xia Bozhen Hu Stan Z. Li 48 0 0 04 Nov 2024
Integrating Graph Neural Networks and Many-Body Expansion Theory for Potential Energy Surfaces Siqi Chen Zhiqiang Wang Xianqi Deng Yili Shen C. Ju ... Lin Xiong Guo Ling Dieaa Alhmoud Hui Guan Zhou Lin 38 0 0 03 Nov 2024
MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language Yoel Shoshan Moshiko Raboh Michal Ozery-Flato Vadim Ratner Alex Golts ... Sharon Kurant Joseph A. Morrone Parthasarathy Suryanarayanan Michal Rosen-Zvi Efrat Hexter 36 1 0 28 Oct 2024
Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization Zichen Wang Yaokun Ji Jianing Tian Shuangjia Zheng DiffM 35 0 0 19 Oct 2024
Are High-Degree Representations Really Unnecessary in Equivariant Graph Neural Networks? Jiacheng Cen Anyi Li Ning Lin Yuxiang Ren Zihe Wang Wenbing Huang 46 2 0 15 Oct 2024
KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction Longlong Li Yipeng Zhang Guanghui Wang Kelin Xia 37 3 0 15 Oct 2024
ProteinBench: A Holistic Evaluation of Protein Foundation Models Fei Ye Zaixiang Zheng Dongyu Xue Yuning Shen Lihao Wang Yiming Ma Yan Wang Qing Guo Xiangxin Zhou Quanquan Gu ELM 48 6 0 10 Sep 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 53 15 0 02 Jun 2024
HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning Rong Han Wenbing Huang Lingxiao Luo Xinyan Han Jiaming Shen Qing Cui Jun Zhou Ting Chen 47 2 0 02 Apr 2024
Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization Xiangxin Zhou Dongyu Xue Ruizhe Chen Zaixiang Zheng Liang Wang Quanquan Gu DiffM 53 20 0 25 Mar 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 38 20 0 01 Mar 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 31 26 0 13 Feb 2024
Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation Divya Nori Simon Mathis Amir Shanehsazzadeh 33 0 0 07 Dec 2023
AI driven B-cell Immunotherapy Design B. M. D. Silva David B. Ascher Nicholas Geard Douglas E. V. Pires 45 0 0 03 Sep 2023
AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies Karolis Martinkus J. Ludwiczak Kyunghyun Cho Weishao Lian J. Lafrance-Vanasse ... A. Rajpal Yunsheng Wu Richard Bonneau Vladimir Gligorijević Andreas Loukas DiffM 39 37 0 28 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
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction Yang Zhang Zhewei Wei Yefei Yuan Zhaohan Ding Wenbing Huang 39 16 0 23 Feb 2023