Learning from Protein Structure with Geometric Vector Perceptrons

3 September 2020

Bowen Jing

Stephan Eismann

Patricia Suriana

Raphael J. L. Townshend

Papers citing "Learning from Protein Structure with Geometric Vector Perceptrons"

50 / 57 papers shown

Title
Combating the Bucket Effect:Multi-Knowledge Alignment for Medication Recommendation Xiang Li Haixu Ma Guanyong Wu Shi Mu C. Li Shunpan Liang 29 0 0 25 Apr 2025
Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems Yunyang Li Zaishuo Xia Lin Huang Xinran Wei Han Yang ... Zun Wang Chang-Shu Liu Jia Zhang Bin Shao Mark B. Gerstein 68 0 0 26 Feb 2025
A Survey of Graph Transformers: Architectures, Theories and Applications Chaohao Yuan Kangfei Zhao Ercan Engin Kuruoglu Liang Wang Tingyang Xu Wenbing Huang Deli Zhao Hong Cheng Yu Rong 49 4 0 23 Feb 2025
UniZyme: A Unified Protein Cleavage Site Predictor Enhanced with Enzyme Active-Site Knowledge Chenao Li Shuo Yan Enyan Dai 49 0 0 10 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
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models Kiwoong Yoo Owen Oertell Junhyun Lee Sanghoon Lee Jaewoo Kang 31 0 0 28 Oct 2024
Structure Language Models for Protein Conformation Generation Jiarui Lu Xiaoyin Chen Stephen Zhewen Lu Chence Shi Hongyu Guo Yoshua Bengio J. Tang DiffM 34 2 0 24 Oct 2024
Beyond Sequence: Impact of Geometric Context for RNA Property Prediction Junjie Xu Artem Moskalev Tommaso Mansi Mangal Prakash Rui Liao AI4CE 26 1 0 15 Oct 2024
Generative Flows on Synthetic Pathway for Drug Design Seonghwan Seo Minsu Kim Tony Shen Martin Ester Jinkyoo Park Sungsoo Ahn Woo Youn Kim 37 3 0 06 Oct 2024
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning Jiaqing Xie Yue Zhao 33 0 0 02 Oct 2024
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction Rong Han Xiaohong Liu Tong Pan Jing Xu Xiaoyu Wang ... Zhenyu Li Zixuan Wang Jiangning Song Guangyu Wang Ting Chen 19 0 0 21 Aug 2024
ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding Yijia Xiao Edward Sun Yiqiao Jin Qifan Wang Wei Wang 40 9 0 21 Aug 2024
Sampling Foundational Transformer: A Theoretical Perspective Viet Anh Nguyen Minh Lenhat Khoa Nguyen Duong Duc Hieu Dao Huu Hung Truong Son-Hy 42 0 0 11 Aug 2024
On the Expressive Power of Sparse Geometric MPNNs Yonatan Sverdlov Nadav Dym 40 1 0 02 Jul 2024
SE(3)-Hyena Operator for Scalable Equivariant Learning Artem Moskalev Mangal Prakash Rui Liao Tommaso Mansi 44 2 0 01 Jul 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 36 12 0 19 Jun 2024
Geometric-informed GFlowNets for Structure-Based Drug Design Grayson Lee Tony Shen Martin Ester 27 0 0 16 Jun 2024
Clustering for Protein Representation Learning Ruijie Quan Wenguan Wang Fan Ma Hehe Fan Yi Yang 24 5 0 30 Mar 2024
Pioneering SE(2)-Equivariant Trajectory Planning for Automated Driving Steffen Hagedorn Marcel Milich A. P. Condurache 36 4 0 17 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
ProtChatGPT: Towards Understanding Proteins with Large Language Models Chao Wang Hehe Fan Ruijie Quan Yi Yang 26 12 0 15 Feb 2024
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design Chuanrui Wang Bozitao Zhong Zuobai Zhang Narendra Chaudhary Sanchit Misra Jian Tang 25 5 0 30 Nov 2023
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Ian Dunn D. Koes DiffM GNN 19 3 0 22 Nov 2023
H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing Gian Marco Visani William Galvin Michael N. Pun Armita Nourmohammad 17 5 0 15 Nov 2023
Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning Shuxin Zheng Jiyan He Chang-Shu Liu Yu Shi Ziheng Lu ... Peiran Jin Chi Chen Frank Noé Haiguang Liu Tie-Yan Liu AI4CE 15 40 0 08 Jun 2023
Multi-level Protein Representation Learning for Blind Mutational Effect Prediction Y. Tan Bingxin Zhou Yuanhong Jiang Yu Wang Liang Hong 21 2 0 08 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 20 13 0 02 Jun 2023
Is novelty predictable? Clara Fannjiang Jennifer Listgarten AI4CE 17 14 0 01 Jun 2023
Inverse Protein Folding Using Deep Bayesian Optimization N. Maus Yimeng Zeng Daniel A. Anderson Phillip M. Maffettone Aaron C. Solomon Peyton Greenside Osbert Bastani Jacob R. Gardner 15 2 0 25 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
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 29 14 0 21 Apr 2023
Accurate and Definite Mutational Effect Prediction with Lightweight Equivariant Graph Neural Networks Bingxin Zhou Outongyi Lv Kai Yi Xinye Xiong P. Tan Liang Hong Yu Wang 20 4 0 13 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 24 0 0 05 Apr 2023
GeoTMI:Predicting quantum chemical property with easy-to-obtain geometry via positional denoising Hyeonsu Kim Jeheon Woo Seonghwan Kim Seokhyun Moon Jun Hyeong Kim Woo Youn Kim AI4CE 28 6 0 28 Mar 2023
EqMotion: Equivariant Multi-agent Motion Prediction with Invariant Interaction Reasoning Chenxin Xu R. Tan Yuhong Tan Siheng Chen Yu Wang Xinchao Wang Yanfeng Wang 27 96 0 20 Mar 2023
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability Zhiqiang Zhong A. Barkova Davide Mottin 14 8 0 16 Feb 2023
A Text-guided Protein Design Framework Shengchao Liu Yanjing Li Zhuoxinran Li A. Gitter Yutao Zhu ... Arvind Ramanathan Chaowei Xiao Jian Tang Hongyu Guo Anima Anandkumar 60 61 0 09 Feb 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 24 14 0 05 Feb 2023
Complete Neural Networks for Complete Euclidean Graphs Snir Hordan Tal Amir S. Gortler Nadav Dym 3DPC 24 5 0 31 Jan 2023
Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds Yeqing Lin Mohammed AlQuraishi DiffM AI4CE 12 73 0 29 Jan 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts Minghao Xu Xinyu Yuan Santiago Miret Jian Tang AI4TS 25 93 0 28 Jan 2023
A Survey on Protein Representation Learning: Retrospect and Prospect Lirong Wu Yu-Feng Huang H. Lin Stan Z. Li AI4TS 20 12 0 31 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 25 32 0 07 Dec 2022
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding Haitao Lin Yufei Huang Odin Zhang Siqi Ma Meng Liu X. Li Lirong Wu Shuiwang Ji Tingjun Hou Stan Z. Li DiffM 16 60 0 21 Nov 2022
Protein Sequence and Structure Co-Design with Equivariant Translation Chence Shi Chuanrui Wang Jiarui Lu Bozitao Zhong Jian Tang DiffM 17 47 0 17 Oct 2022
Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design Keir Adams Connor W. Coley 34 25 0 06 Oct 2022
AlphaFold Distillation for Protein Design Igor Melnyk A. Lozano Payel Das Vijil Chenthamarakshan 12 1 0 05 Oct 2022
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model Zhuoran Qiao Weili Nie Arash Vahdat Thomas F. Miller Anima Anandkumar DiffM 31 84 0 30 Sep 2022
PiFold: Toward effective and efficient protein inverse folding Zhangyang Gao Cheng Tan Pablo Chacón Stan Z. Li AI4CE 61 104 0 22 Sep 2022
Torsional Diffusion for Molecular Conformer Generation Bowen Jing Gabriele Corso Jeffrey Chang Regina Barzilay Tommi Jaakkola DiffM BDL 25 259 0 01 Jun 2022