Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design

9 October 2021

Papers citing "Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design"

50 / 57 papers shown

Title
Compositional Flows for 3D Molecule and Synthesis Pathway Co-design Tony Shen Seonghwan Seo Ross Irwin Kieran Didi Simon Olsson Woo Youn Kim Martin Ester 51 0 0 10 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 43 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 44 0 0 11 Feb 2025
Decoupled Sequence and Structure Generation for Realistic Antibody Design Nayoung Kim Minsu Kim Sungsoo Ahn Jinkyoo Park 47 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 42 1 0 31 Dec 2024
S^2 ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learning Mingze Yin Hanjing Zhou Jialu Wu Yiheng Zhu Yuxuan Zhan ... Hongxia Xu Chang-Yu Hsieh J. Chen Tingjun Hou Jian Wu 72 0 0 20 Nov 2024
SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation Liang He Peiran Jin Yaosen Min Shufang Xie Lijun Wu Tao Qin Xiaozhuan Liang Kaiyuan Gao Yuliang Jiang Tie-Yan Liu AI4TS 25 1 0 31 Oct 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 26 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 30 0 0 19 Oct 2024
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
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding Yijia Xiao Edward Sun Yiqiao Jin Qifan Wang Wei Wang 47 10 0 21 Aug 2024
Evaluating representation learning on the protein structure universe Arian R. Jamasb Alex Morehead Chaitanya K. Joshi Zuobai Zhang Kieran Didi ... Charles Harris Jian Tang Jianlin Cheng Pietro Lio Tom L. Blundell SSL 48 12 0 19 Jun 2024
AntibodyFlow: Normalizing Flow Model for Designing Antibody Complementarity-Determining Regions Bohao Xu Y Samuel Wang Wenyu Chen Shimin Shan OOD 23 0 0 19 Jun 2024
Topological Neural Networks go Persistent, Equivariant, and Continuous Yogesh Verma Amauri H Souza Vikas K. Garg AI4CE 43 4 0 05 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 45 15 0 02 Jun 2024
RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching Divya Nori Wengong Jin AI4CE 47 8 0 29 May 2024
De novo antibody design with SE(3) diffusion Daniel Cutting Frédéric A. Dreyer David Errington Constantin Schneider Charlotte M. Deane DiffM 38 3 0 13 May 2024
Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization Xiangxin Zhou Dongyu Xue Ruizhe Chen Zaixiang Zheng Liang Wang Quanquan Gu DiffM 42 19 0 25 Mar 2024
SGNet: Folding Symmetrical Protein Complex with Deep Learning Zhaoqun Li Jingcheng Yu Qiwei Ye 23 0 0 07 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 34 20 0 01 Mar 2024
Deep Confident Steps to New Pockets: Strategies for Docking Generalization Gabriele Corso Arthur Deng Benjamin Fry Nicholas Polizzi Regina Barzilay Tommi Jaakkola OOD 45 27 0 28 Feb 2024
ProtChatGPT: Towards Understanding Proteins with Large Language Models Chao Wang Hehe Fan Ruijie Quan Yi Yang 26 13 0 15 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
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design Fang Wu Stan Z. Li 33 17 0 30 Oct 2023
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola 37 25 0 09 Oct 2023
AI driven B-cell Immunotherapy Design B. M. D. Silva David B. Ascher Nicholas Geard Douglas E. V. Pires 37 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 Yongpeng Wu Richard Bonneau Vladimir Gligorijević Andreas Loukas DiffM 31 37 0 28 Jul 2023
Multi-Task Learning with Loop Specific Attention for CDR Structure Prediction Eleni Giovanoudi Dimitrios Rafailidis 11 1 0 22 Jun 2023
Protein Discovery with Discrete Walk-Jump Sampling Nathan C. Frey Daniel Berenberg Karina Zadorozhny J. Kleinhenz J. Lafrance-Vanasse ... Richard Bonneau Kyunghyun Cho Andreas Loukas Vladimir Gligorijević Saeed Saremi DiffM 16 33 0 08 Jun 2023
Multi-level Protein Representation Learning for Blind Mutational Effect Prediction Y. Tan Bingxin Zhou Yuanhong Jiang Yu Wang Liang Hong 26 2 0 08 Jun 2023
AbODE: Ab Initio Antibody Design using Conjoined ODEs Yogesh Verma Markus Heinonen Vikas K. Garg 29 18 0 31 May 2023
Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files Daniel Flam-Shepherd Alán Aspuru-Guzik 27 51 0 09 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
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 35 0 0 05 Apr 2023
IGB: Addressing The Gaps In Labeling, Features, Heterogeneity, and Size of Public Graph Datasets for Deep Learning Research Arpandeep Khatua Vikram Sharma Mailthody Bhagyashree Taleka Tengfei Ma Xiang Song Wen-mei W. Hwu AI4CE 48 37 0 27 Feb 2023
Structure-informed Language Models Are Protein Designers Zaixiang Zheng Yifan Deng Dongyu Xue Yi Zhou YE Fei Quanquan Gu 29 87 0 03 Feb 2023
End-to-End Full-Atom Antibody Design Xiangzhe Kong Wenbing Huang Yang Liu 22 49 0 01 Feb 2023
Curvature Filtrations for Graph Generative Model Evaluation Joshua Southern Jeremy Wayland Michael M. Bronstein Bastian Alexander Rieck 23 14 0 30 Jan 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 21 19 0 22 Jan 2023
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design Kaiyuan Gao Lijun Wu Jinhua Zhu Tianbo Peng Yingce Xia ... Shufang Xie Tao Qin Haiguang Liu Kun He Tie-Yan Liu 24 9 0 26 Oct 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 27 47 0 17 Oct 2022
Reprogramming Pretrained Language Models for Antibody Sequence Infilling Igor Melnyk Vijil Chenthamarakshan Pin-Yu Chen Payel Das Amit Dhurandhar Inkit Padhi Devleena Das 25 28 0 05 Oct 2022
AlphaFold Distillation for Protein Design Igor Melnyk A. Lozano Payel Das Vijil Chenthamarakshan 12 1 0 05 Oct 2022
Structured Q-learning For Antibody Design Alexander I. Cowen-Rivers P. Gorinski Aivar Sootla Asif R. Khan Liu Furui Jun Wang Jan Peters H. Ammar OffRL OnRL 26 3 0 10 Sep 2022
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
Conditional Antibody Design as 3D Equivariant Graph Translation Xiangzhe Kong Wenbing Huang Yang Liu DiffM 32 84 0 12 Aug 2022
Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement Wengong Jin Regina Barzilay Tommi Jaakkola 14 22 0 14 Jul 2022
EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures Alex Morehead Xiao Chen Tianqi Wu Jian Liu Jianlin Cheng 44 7 0 20 May 2022