Multi-Scale Representation Learning on Proteins

4 April 2022

Papers citing "Multi-Scale Representation Learning on Proteins"

42 / 42 papers shown

Title
Bidirectional Hierarchical Protein Multi-Modal Representation Learning Xuefeng Liu Songhao Jiang Chih-chan Tien J. Xu Rick L. Stevens 25 0 0 07 Apr 2025
QuickBind: A Light-Weight And Interpretable Molecular Docking Model Wojtek Treyde Seohyun Chris Kim N. Bouatta Mohammed AlQuraishi 30 0 0 21 Oct 2024
Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches Xuefeng Liu Songhao Jiang Xiaotian Duan Archit Vasan Chong Liu ... Heng Ma Thomas Brettin Fangfang Xia Ian Foster Rick L. Stevens AI4CE 34 0 0 30 Sep 2024
Advanced atom-level representations for protein flexibility prediction utilizing graph neural networks Sina Sarparast Aldo Zaimi Maximilian Ebert Michael-Rock Goldsmith AI4CE 35 0 0 22 Aug 2024
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction Yuyan Ni Shikun Feng Xin Hong Yuancheng Sun Wei-Ying Ma Zhiming Ma Qiwei Ye Yanyan Lan AI4CE 41 10 0 14 Jul 2024
Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs Michail Chatzianastasis George Dasoulas Michalis Vazirgiannis SSL 24 0 0 20 Jun 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
A Cross-Field Fusion Strategy for Drug-Target Interaction Prediction Hongzhi Zhang Xiuwen Gong Shirui Pan Jia Wu Bo Du Wenbin Hu 26 3 0 23 May 2024
Exploiting Hierarchical Interactions for Protein Surface Learning Yiqun Lin Liang Pan Yi Li Ziwei Liu Xiaomeng Li 40 1 0 17 Jan 2024
Causal Optimal Transport of Abstractions Yorgos Felekis Fabio Massimo Zennaro Nicola Branchini Theodoros Damoulas CML OT 53 5 0 13 Dec 2023
Target-Free Compound Activity Prediction via Few-Shot Learning Peter Eckmann Jake Anderson Michael K. Gilson Rose Yu 22 1 0 27 Nov 2023
Protein-ligand binding representation learning from fine-grained interactions Shikun Feng Minghao Li Yinjun Jia Wei-Ying Ma Yanyan Lan SSL AI4CE 24 8 0 09 Nov 2023
ProFSA: Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment Bowen Gao Yinjun Jia Yuanle Mo Yuyan Ni Wei-Ying Ma Zhiming Ma Yanyan Lan 22 7 0 11 Oct 2023
AtomSurf : Surface Representation for Learning on Protein Structures Vincent Mallet Souhaib Attaiki M. Ovsjanikov 42 3 0 28 Sep 2023
Mixup-Augmented Meta-Learning for Sample-Efficient Fine-Tuning of Protein Simulators Jingbang Chen Yian Wang Xingwei Qu Shuangjia Zheng Yao-Chun Yang Hao Dong Jie Fu 25 0 0 29 Aug 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 44 1 0 20 Jun 2023
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations Pengcheng Jiang Cao Xiao Tianfan Fu Jimeng Sun 50 3 0 02 Jun 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
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 46 0 0 05 Apr 2023
Learning Harmonic Molecular Representations on Riemannian Manifold Yiqun Wang Yuning Shen Shih‐Ya Chen Lihao Wang Fei Ye Hao Zhou 43 12 0 27 Mar 2023
3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction Jiaqi Guan Wesley Wei Qian Xingang Peng Yufeng Su Jian-wei Peng Jianzhu Ma DiffM 34 162 0 06 Mar 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 29 8 0 16 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
Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equation Wengong Jin Siranush Sarkizova Xun Chen N. Hacohen Caroline Uhler 29 20 0 25 Jan 2023
Structure-based drug discovery with deep learning Rıza Özçelik D. V. Tilborg José Jiménez-Luna F. Grisoni AI4CE 29 35 0 26 Dec 2022
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
Geometry-Complete Perceptron Networks for 3D Molecular Graphs Alex Morehead Jianlin Cheng GNN 3DV AI4CE 34 12 0 04 Nov 2022
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 53 104 0 19 Oct 2022
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 142 412 0 04 Oct 2022
Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space Gian Marco Visani Michael N. Pun Arman Angaji Armita Nourmohammad BDL 24 3 0 30 Sep 2022
Multimodal learning with graphs Yasha Ektefaie George Dasoulas Ayush Noori Maha Farhat Marinka Zitnik 51 83 0 07 Sep 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
Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement Wengong Jin Regina Barzilay Tommi Jaakkola 22 22 0 14 Jul 2022
Contrastive Representation Learning for 3D Protein Structures Pedro Hermosilla Timo Ropinski 3DV 51 51 0 31 May 2022
EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures Alex Morehead Xiao Chen Tianqi Wu Jian Liu Jianlin Cheng 49 7 0 20 May 2022
Structure-aware Protein Self-supervised Learning Can Chen Jingbo Zhou Fan Wang Xue Liu Dejing Dou SSL 24 65 0 06 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 13 217 0 11 Mar 2022
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk O. Ganea L. Pattanaik Regina Barzilay Tommi Jaakkola 29 262 0 07 Feb 2022
Mitigating cold start problems in drug-target affinity prediction with interaction knowledge transferring T. Nguyen Thin Nguyen T. Tran 22 14 0 16 Jan 2022
Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs Fang Wu Dragomir R. Radev Huabin Xing ViT 36 54 0 04 Oct 2021
Superpixels: An Evaluation of the State-of-the-Art David Stutz Alexander Hermans Bastian Leibe SupR 80 468 0 06 Dec 2016