Contrastive Representation Learning for 3D Protein Structures

31 May 2022

Timo Ropinski

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

23 / 23 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 41 1 0 31 Oct 2024
ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception Mingqing Wang Zhiwei Nie Yonghong He Zhixiang Ren 32 0 0 24 May 2024
Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship Eunji Ko Seul Lee Minseon Kim Dongki Kim 36 0 0 29 Apr 2024
Clustering for Protein Representation Learning Ruijie Quan Wenguan Wang Fan Ma Hehe Fan Yi Yang 29 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 41 5 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 35 11 0 13 Feb 2024
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design Fang Wu Stan Z. Li 33 17 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 41 10 0 18 Oct 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 25 13 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 23 33 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 24 5 0 08 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 41 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 27 30 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 31 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 21 19 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 33 32 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 27 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 36 55 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 13 98 0 05 Jun 2022
3D Graph Contrastive Learning for Molecular Property Prediction Kisung Moon Sunyoung Kwon 18 17 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 13 217 0 11 Mar 2022
Vector Neurons: A General Framework for SO(3)-Equivariant Networks Congyue Deng Or Litany Yueqi Duan A. Poulenard Andrea Tagliasacchi Leonidas J. Guibas 3DPC 123 316 0 25 Apr 2021
ImageNet Large Scale Visual Recognition Challenge Olga Russakovsky Jia Deng Hao Su J. Krause S. Satheesh ... A. Karpathy A. Khosla Michael S. Bernstein Alexander C. Berg Li Fei-Fei VLM ObjD 296 39,217 0 01 Sep 2014