Learning protein sequence embeddings using information from structure

22 February 2019

Papers citing "Learning protein sequence embeddings using information from structure"

50 / 58 papers shown

Title
Prot42: a Novel Family of Protein Language Models for Target-aware Protein Binder Generation Mohammad Amaan Sayeed Engin Tekin Maryam Nadeem Nancy A. ElNaker A. Singh Natalia Vassilieva Boulbaba Ben Amor 28 0 0 06 Apr 2025
Protein Large Language Models: A Comprehensive Survey Yijia Xiao Wanjia Zhao Junkai Zhang Yiqiao Jin Han Zhang ... Xiao Luo Yu-Jie Zhang James Zou Yizhou Sun Wei Wang LM&MA AI4CE 64 3 0 21 Feb 2025
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences Niklas Schmidinger Lisa Schneckenreiter Philipp Seidl Johannes Schimunek Pieter-Jan Hoedt Johannes Brandstetter Andreas Mayr Sohvi Luukkonen Sepp Hochreiter G. Klambauer MedIm 63 4 0 06 Nov 2024
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 39 1 0 31 Oct 2024
Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions Sully F. Chen Robert J. Steele Beakal Lemeneh S. Lad Eric Oermann Eric K. Oermann AI4CE 43 0 0 29 Aug 2024
Structure-Informed Protein Language Model Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 35 8 0 07 Feb 2024
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
Everything Perturbed All at Once: Enabling Differentiable Graph Attacks Haoran Liu Bokun Wang Jianling Wang Xiangjue Dong Tianbao Yang James Caverlee AAML 36 3 0 29 Aug 2023
PoET: A generative model of protein families as sequences-of-sequences Timothy F. Truong Tristan Bepler SLR 21 38 0 09 Jun 2023
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning Xiangzhe Kong Wen-bing Huang Yang Liu 25 13 0 02 Jun 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 41 0 0 05 Apr 2023
Lightweight Contrastive Protein Structure-Sequence Transformation Jiangbin Zheng Ge Wang Yufei Huang Bozhen Hu Siyuan Li Cheng Tan Xinwen Fan Stan Z. Li 30 6 0 19 Mar 2023
Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling Hong-Yu Zhou Yunxiang Fu Zhicheng Zhang Cheng Bian Yizhou Yu 22 8 0 30 Jan 2023
A Survey on Protein Representation Learning: Retrospect and Prospect Lirong Wu Yu-Feng Huang H. Lin Stan Z. Li AI4TS 33 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 33 32 0 07 Dec 2022
Multiscale Graph Neural Networks for Protein Residue Contact Map Prediction Kuang Liu R. Kalia Xinlian Liu A. Nakano K. Nomura P. Vashishta R. Zamora-Resendiz 17 2 0 02 Dec 2022
Protein Language Models and Structure Prediction: Connection and Progression Bozhen Hu Jun Xia Jiangbin Zheng Cheng Tan Yufei Huang Yongjie Xu Stan Z. Li 27 40 0 30 Nov 2022
Training self-supervised peptide sequence models on artificially chopped proteins Gil Sadeh Zichen Wang J. Grewal Huzefa Rangwala Layne Price 26 2 0 09 Nov 2022
Geometry-Complete Perceptron Networks for 3D Molecular Graphs Alex Morehead Jianlin Cheng GNN 3DV AI4CE 32 12 0 04 Nov 2022
Antibody Representation Learning for Drug Discovery Lin Li Esther Gupta J. Spaeth Leslie Shing Tristan Bepler R. Caceres 25 6 0 05 Oct 2022
When Bioprocess Engineering Meets Machine Learning: A Survey from the Perspective of Automated Bioprocess Development Nghia Duong-Trung Stefan Born Jong Woo Kim M. Schermeyer Katharina Paulick ... Thorben Werner Randolf Scholz Lars Schmidt-Thieme Peter Neubauer Ernesto Martinez 34 20 0 02 Sep 2022
Shuffled total least squares Qian Wang D. Sussman 28 2 0 02 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
Exploring evolution-aware & -free protein language models as protein function predictors Min Hu Fajie Yuan Kevin Kaichuang Yang Fusong Ju Jingyu Su Hongya Wang Fei Yang Qiuyang Ding 21 36 0 14 Jun 2022
Contrastive Representation Learning for 3D Protein Structures Pedro Hermosilla Timo Ropinski 3DV 48 51 0 31 May 2022
Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval Pascal Notin M. Dias J. Frazer Javier Marchena-Hurtado Aidan Gomez D. Marks Y. Gal 55 177 0 27 May 2022
ODBO: Bayesian Optimization with Search Space Prescreening for Directed Protein Evolution Lixue Cheng Ziyi Yang Chang-Yu Hsieh Ben Liao Shengyu Zhang 27 6 0 19 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
Multi-Scale Representation Learning on Proteins Vignesh Ram Somnath Charlotte Bunne Andreas Krause 37 91 0 04 Apr 2022
Few Shot Protein Generation Soumya Ram Tristan Bepler 31 6 0 03 Apr 2022
Hypergraph Convolutional Networks via Equivalency between Hypergraphs and Undirected Graphs Jiying Zhang Fuyang Li Xi Xiao Tingyang Xu Yu Rong Junzhou Huang Yatao Bian GNN 13 24 0 31 Mar 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
Encoding protein dynamic information in graph representation for functional residue identification Chiang Yuan Weiwei Hui Shu-Wei Chang 16 7 0 15 Dec 2021
Multimodal Pre-Training Model for Sequence-based Prediction of Protein-Protein Interaction Yang Xue Zijing Liu Xiaomin Fang Fan Wang 17 8 0 09 Dec 2021
Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model Liang He Shizhuo Zhang Lijun Wu Huanhuan Xia Fusong Ju ... Jianwei Zhu Pan Deng Bin Shao Tao Qin Tie-Yan Liu 26 31 0 29 Oct 2021
Pre-trained Language Models in Biomedical Domain: A Systematic Survey Benyou Wang Qianqian Xie Jiahuan Pei Zhihong Chen Prayag Tiwari Zhao Li Jie Fu LM&MA AI4CE 37 163 0 11 Oct 2021
Machine learning modeling of family wide enzyme-substrate specificity screens Samuel Goldman Ria Das Kevin Kaichuang Yang Connor W. Coley 25 54 0 08 Sep 2021
Adaptive Residue-wise Profile Fusion for Low Homologous Protein SecondaryStructure Prediction Using External Knowledge Qin Wang JunChao Wei Boyuan Wang Zhen Li Sheng Wang Shuguang Cui 15 1 0 05 Aug 2021
Adaptive machine learning for protein engineering B. Hie Kevin Kaichuang Yang 27 80 0 10 Jun 2021
Random Embeddings and Linear Regression can Predict Protein Function Tianyu Lu Alex X. Lu Alan M. Moses SSL 24 5 0 25 Apr 2021
Protein sequence design with deep generative models Zachary Wu Kadina E. Johnston F. Arnold Kevin Kaichuang Yang 19 134 0 09 Apr 2021
Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning Amy X. Lu Alex X. Lu Alan M. Moses SSL 27 13 0 25 Dec 2020
DenseHMM: Learning Hidden Markov Models by Learning Dense Representations Joachim Sicking Maximilian Pintz Maram Akila Tim Wirtz 11 1 0 17 Dec 2020
Pre-training Protein Language Models with Label-Agnostic Binding Pairs Enhances Performance in Downstream Tasks Modestas Filipavicius Matteo Manica Joris Cadow María Rodríguez Martínez 18 13 0 05 Dec 2020
Profile Prediction: An Alignment-Based Pre-Training Task for Protein Sequence Models Pascal Sturmfels Jesse Vig Ali Madani Nazneen Rajani 15 24 0 01 Dec 2020
What is a meaningful representation of protein sequences? N. Detlefsen Søren Hauberg Wouter Boomsma 10 111 0 28 Nov 2020
Is Transfer Learning Necessary for Protein Landscape Prediction? Amir Shanehsazzadeh David Belanger David Dohan SSL 12 61 0 31 Oct 2020
Fixed-Length Protein Embeddings using Contextual Lenses Amir Shanehsazzadeh David Belanger David Dohan 12 1 0 15 Oct 2020
MutaGAN: A Seq2seq GAN Framework to Predict Mutations of Evolving Protein Populations D. S. Berman Craig Howser T. Mehoke Jared D. Evans 32 9 0 26 Aug 2020
ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing Ahmed Elnaggar M. Heinzinger Christian Dallago Ghalia Rehawi Yu Wang ... Tamas B. Fehér Christoph Angerer Martin Steinegger D. Bhowmik B. Rost DRL 20 917 0 13 Jul 2020