Contrastive Representation Learning for 3D Protein Structures

31 May 2022

Timo Ropinski

Papers citing "Contrastive Representation Learning for 3D Protein Structures"

21 / 21 papers shown

Title
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 80 2 0 31 Oct 2024
ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception Mingqing Wang Zhiwei Nie Yonghong He Zhixiang Ren 69 0 0 24 May 2024
Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship Eunji Ko Seul Lee Minseon Kim Dongki Kim 61 0 0 29 Apr 2024
Clustering for Protein Representation Learning Ruijie Quan Wenguan Wang Fan Ma Hehe Fan Yi Yang 102 5 0 30 Mar 2024
ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling Kangjie Zheng Siyu Long Tianyu Lu Junwei Yang Xinyu Dai Ming Zhang Zaiqing Nie Wei-Ying Ma Hao Zhou 75 10 0 05 Mar 2024
PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction Lirong Wu Yufei Huang Cheng Tan Zhangyang Gao Bozhen Hu Haitao Lin Zicheng Liu Stan Z. Li 69 11 0 13 Feb 2024
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design Fang Wu Stan Z. Li 82 18 0 30 Oct 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 63 14 0 18 Oct 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 158 15 0 02 Jun 2023
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing Yang Zhang Zuobai Zhang Bozitao Zhong Sanchit Misra Jian Tang DiffM 108 35 0 01 Jun 2023
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems Fang Wu Huiling Qin Siyuan Li Stan Z. Li Xianyuan Zhan Jinbo Xu 80 5 0 08 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 210 0 0 05 Apr 2023
A Systematic Study of Joint Representation Learning on Protein Sequences and Structures Zuobai Zhang Chuanrui Wang Minghao Xu Vijil Chenthamarakshan A. Lozano Payel Das Jian Tang 83 32 0 11 Mar 2023
Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy Yufei Huang Lirong Wu Haitao Lin Jiangbin Zheng Ge Wang Stan Z. Li DiffM 81 14 0 05 Feb 2023
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction Zuobai Zhang Minghao Xu A. Lozano Vijil Chenthamarakshan Payel Das Jian Tang DiffM 90 22 0 28 Jan 2023
Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks Fang Wu Yujun Tao Dragomir R. Radev Jinbo Xu Stan Z. Li AI4CE 105 34 0 07 Dec 2022
EurNet: Efficient Multi-Range Relational Modeling of Spatial Multi-Relational Data Minghao Xu Yuanfan Guo Yi Xu Jiangtao Tang Xinlei Chen Yuandong Tian GNN 70 6 0 23 Nov 2022
Learning Hierarchical Protein Representations via Complete 3D Graph Networks Limei Wang Haoran Liu Yi Liu Jerry Kurtin Shuiwang Ji GNN 75 60 0 26 Jul 2022
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding Minghao Xu Zuobai Zhang Jiarui Lu Zhaocheng Zhu Yang Zhang Chang Ma Runcheng Liu Jian Tang 76 108 0 05 Jun 2022
3D Graph Contrastive Learning for Molecular Property Prediction Kisung Moon Sunyoung Kwon 68 19 0 31 May 2022
Protein Representation Learning by Geometric Structure Pretraining Zuobai Zhang Minghao Xu Arian R. Jamasb Vijil Chenthamarakshan A. Lozano Payel Das Jian Tang SSL 141 234 0 11 Mar 2022