DeepSF: deep convolutional neural network for mapping protein sequences to folds

4 June 2017

Papers citing "DeepSF: deep convolutional neural network for mapping protein sequences to folds"

50 / 52 papers shown

Title
Prot2Token: A Unified Framework for Protein Modeling via Next-Token Prediction Mahdi Pourmirzaei Farzaneh Esmaili Salhuldin Alqarghuli Mohammadreza Pourmirzaei Ye Han Kai Chen Mohsen Rezaei Duolin Wang Dong Xu 15 0 0 26 May 2025
A Comprehensive Benchmark for RNA 3D Structure-Function Modeling Luis Wyss Vincent Mallet Wissam Karroucha Karsten Borgwardt Carlos Oliver 104 0 0 27 Mar 2025
Protein Structure Tokenization: Benchmarking and New Recipe Xinyu Yuan Zichen Wang Marcus Collins Huzefa Rangwala 62 1 0 28 Feb 2025
SeqProFT: Applying LoRA Finetuning for Sequence-only Protein Property Predictions Shuo Zhang Jian K. Liu 110 1 0 18 Nov 2024
Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer Zihan Pengmei Zhengyuan Shen Zichen Wang Marcus Collins Huzefa Rangwala AI4CE 55 2 0 29 Oct 2024
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning Jiaqing Xie Yue Zhao 134 1 0 02 Oct 2024
GOProteinGNN: Leveraging Protein Knowledge Graphs for Protein Representation Learning Dan Kalifa Uriel Singer Kira Radinsky 143 1 0 31 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 115 13 0 19 Jun 2024
Clustering for Protein Representation Learning Ruijie Quan Wenguan Wang Fan Ma Hehe Fan Yi Yang 85 5 0 30 Mar 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 89 31 0 13 Feb 2024
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 41 1 0 10 Feb 2024
Structure-Informed Protein Language Model Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 50 9 0 07 Feb 2024
Endowing Protein Language Models with Structural Knowledge Dexiong Chen Philip Hartout Paolo Pellizzoni Carlos Oliver Karsten Borgwardt 100 13 0 26 Jan 2024
xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein Bo Chen Xingyi Cheng Pan Li Yangli-ao Geng Jing Gong ... Chiming Liu Aohan Zeng Yuxiao Dong Jie Tang Leo T. Song 81 112 0 11 Jan 2024
PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications Yang Tan Mingchen Li P. Tan Ziyi Zhou Huiqun Yu Guisheng Fan Liang Hong 60 0 0 26 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 56 14 0 18 Oct 2023
InstructProtein: Aligning Human and Protein Language via Knowledge Instruction Zeyuan Wang Qiang Zhang Keyan Ding Ming Qin Zhuang Xiang Xiaotong Li Huajun Chen 99 32 0 05 Oct 2023
Ophiuchus: Scalable Modeling of Protein Structures through Hierarchical Coarse-graining SO(3)-Equivariant Autoencoders Allan dos Santos Costa Ilan Mitnikov Mario Geiger Manvitha Ponnapati Tess E. Smidt Joseph Jacobson DiffM 47 3 0 04 Oct 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Zhiling Zheng ... Anima Anandkumar C. Borgs J. Chayes Hongyu Guo Jian Tang AI4CE 94 24 0 15 Jun 2023
DelBugV: Delta-Debugging Neural Network Verifiers R. Elsaleh Guy Katz 101 2 0 29 May 2023
Retrieved Sequence Augmentation for Protein Representation Learning Chang Ma Haiteng Zhao Lin Zheng Jiayi Xin Qintong Li Lijun Wu Zhihong Deng Yang Lu Qi Liu Lingpeng Kong AI4TS 64 10 0 24 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 128 70 0 09 Feb 2023
Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling Hong-Yu Zhou Yunxiang Fu Zhicheng Zhang Cheng Bian Yizhou Yu 77 8 0 30 Jan 2023
Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling Ahmed Elnaggar Hazem Essam Wafaa Salah-Eldin Walid Moustafa Mohamed Elkerdawy Charlotte Rochereau B. Rost 233 102 0 16 Jan 2023
Reprogramming Pretrained Language Models for Protein Sequence Representation Learning R. Vinod Pin-Yu Chen Payel Das 137 14 0 05 Jan 2023
Learning Hierarchical Protein Representations via Complete 3D Graph Networks Limei Wang Haoran Liu Yi Liu Jerry Kurtin Shuiwang Ji GNN 60 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 58 108 0 05 Jun 2022
Contrastive Representation Learning for 3D Protein Structures Pedro Hermosilla Timo Ropinski 3DV 110 54 0 31 May 2022
Structure-aware Protein Self-supervised Learning Can Chen Jingbo Zhou Fan Wang Xue Liu Dejing Dou SSL 91 68 0 06 Apr 2022
Multi-Scale Representation Learning on Proteins Vignesh Ram Somnath Charlotte Bunne Andreas Krause 75 96 0 04 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 63 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 86 233 0 11 Mar 2022
Improving Molecular Representation Learning with Metric Learning-enhanced Optimal Transport Fang Wu Nicolas Courty Shuting Jin Stan Z. Li OOD OT 81 8 0 13 Feb 2022
Don't Sweep your Learning Rate under the Rug: A Closer Look at Cross-modal Transfer of Pretrained Transformers Dan Rothermel Margaret Li Tim Rocktaschel Jakob N. Foerster 70 6 0 26 Jul 2021
Structure Inducing Pre-Training Matthew B. A. McDermott Brendan Yap Peter Szolovits Marinka Zitnik 82 21 0 18 Mar 2021
Pretrained Transformers as Universal Computation Engines Kevin Lu Aditya Grover Pieter Abbeel Igor Mordatch 71 221 0 09 Mar 2021
Profile Prediction: An Alignment-Based Pre-Training Task for Protein Sequence Models Pascal Sturmfels Jesse Vig Ali Madani Nazneen Rajani 73 25 0 01 Dec 2020
What is a meaningful representation of protein sequences? N. Detlefsen Søren Hauberg Wouter Boomsma 115 115 0 28 Nov 2020
Transfer Learning for Protein Structure Classification at Low Resolution Alexander Hudson S. Gong 54 1 0 11 Aug 2020
Deep Learning in Protein Structural Modeling and Design Wenhao Gao S. Mahajan Jeremias Sulam Jeffrey J. Gray 84 160 0 16 Jul 2020
Machine-Learning Driven Drug Repurposing for COVID-19 Semih Cantürk Aman Singh P. St-Amant Jason Behrmann 31 10 0 25 Jun 2020
A Trainable Optimal Transport Embedding for Feature Aggregation and its Relationship to Attention Grégoire Mialon Dexiong Chen Alexandre d’Aspremont Julien Mairal OT 42 0 0 22 Jun 2020
Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery Hakime Öztürk Arzucan Özgür P. Schwaller Teodoro Laino Elif Özkirimli 87 121 0 10 Feb 2020
Macromolecule Classification Based on the Amino-acid Sequence F. Ghaffar Sarwar Khan O. Gaddisa Chen Yu-jhen 35 0 0 06 Jan 2020
Performance of regression models as a function of experiment noise Gang Li Jan Zrimec B. Ji Jun Geng J. Larsbrink Aleksej Zelezniak Jens Nielsen M. Engqvist 49 19 0 17 Dec 2019
Learning protein conformational space by enforcing physics with convolutions and latent interpolations Venkatakrishnan Ramaswamy Chris G. Willcocks M. Degiacomi 39 3 0 10 Oct 2019
Recurrent Neural Network-based Model for Accelerated Trajectory Analysis in AIMD Simulations M. Eslamibidgoli Mehrdad Mokhtari M. Eikerling 51 13 0 23 Sep 2019
Classification of Macromolecule Type Based on Sequences of Amino Acids Using Deep Learning Sarwar Khan F. Ghaffar Imad Ali Qazi Mazhar 42 0 0 01 Jul 2019
Evaluating Protein Transfer Learning with TAPE Roshan Rao Nicholas Bhattacharya Neil Thomas Yan Duan Xi Chen John F. Canny Pieter Abbeel Yun S. Song SSL 108 809 0 19 Jun 2019
Recurrent Kernel Networks Dexiong Chen Laurent Jacob Julien Mairal 91 13 0 07 Jun 2019