Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design

24 June 2021

Yue Cao

Payel Das

Vijil Chenthamarakshan

Papers citing "Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design"

20 / 20 papers shown

Title
Protein Large Language Models: A Comprehensive Survey Yijia Xiao Wanjia Zhao Junkai Zhang Yiqiao Jin Han Zhang ... Xiao Luo Yu-Jie Zhang James Y. Zou Y. Sun Wei Wang LM&MA AI4CE 54 3 0 21 Feb 2025
Clustering for Protein Representation Learning Ruijie Quan Wenguan Wang Fan Ma Hehe Fan Yi Yang 29 5 0 30 Mar 2024
TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation Zongying Lin Hao Li Liuzhenghao Lv Lin Bin Junwu Zhang Calvin Yu-Chian Chwn Li Yuan Tian Yonghong 24 3 0 27 Feb 2024
Efficiently Predicting Protein Stability Changes Upon Single-point Mutation with Large Language Models Yijie Zhang Zhangyang Gao Cheng Tan Stan Z.Li 27 2 0 07 Dec 2023
De novo protein design using geometric vector field networks Weian Mao Muzhi Zhu Zheng Sun Shuaike Shen Lin Yuanbo Wu Hao Chen Chunhua Shen DiffM 33 10 0 18 Oct 2023
AbODE: Ab Initio Antibody Design using Conjoined ODEs Yogesh Verma Markus Heinonen Vikas K. Garg 26 18 0 31 May 2023
Knowledge-Design: Pushing the Limit of Protein Design via Knowledge Refinement Zhangyang Gao Cheng Tan Stan Z. Li 21 15 0 20 May 2023
Protein Language Models and Structure Prediction: Connection and Progression Bozhen Hu Jun-Xiong Xia Jiangbin Zheng Cheng Tan Yufei Huang Yongjie Xu Stan Z. Li 19 40 0 30 Nov 2022
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 22 9 0 26 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 19 28 0 05 Oct 2022
AlphaFold Distillation for Protein Design Igor Melnyk A. Lozano Payel Das Vijil Chenthamarakshan 12 1 0 05 Oct 2022
PiFold: Toward effective and efficient protein inverse folding Zhangyang Gao Cheng Tan Pablo Chacón Stan Z. Li AI4CE 65 104 0 22 Sep 2022
Conditional Antibody Design as 3D Equivariant Graph Translation Xiangzhe Kong Wenbing Huang Yang Liu DiffM 19 84 0 12 Aug 2022
Learning Hierarchical Protein Representations via Complete 3D Graph Networks Limei Wang Haoran Liu Yi Liu Jerry Kurtin Shuiwang Ji GNN 28 55 0 26 Jul 2022
Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement Wengong Jin Regina Barzilay Tommi Jaakkola 14 21 0 14 Jul 2022
Generative De Novo Protein Design with Global Context Cheng Tan Zhangyang Gao Jun-Xiong Xia Bozhen Hu Stan Z. Li 4 7 0 21 Apr 2022
Protein Representation Learning by Geometric Structure Pretraining Zuobai Zhang Minghao Xu Arian R. Jamasb Vijil Chenthamarakshan A. Lozano Payel Das Jian Tang SSL 11 217 0 11 Mar 2022
AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation M. A. Khan Alexander I. Cowen-Rivers Antoine Grosnit Derrick-Goh-Xin Deik Philippe A. Robert ... Rasul Tutunov Dany Bou-Ammar Jun Wang Amos Storkey Haitham Bou-Ammar 45 22 0 29 Jan 2022
Benchmarking deep generative models for diverse antibody sequence design Igor Melnyk Payel Das Vijil Chenthamarakshan A. Lozano DiffM 40 17 0 12 Nov 2021
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design Wengong Jin Jeremy Wohlwend Regina Barzilay Tommi Jaakkola 11 136 0 09 Oct 2021