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Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

2 September 2016

Papers citing "Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model"

50 / 54 papers shown

Title
BioArc: Discovering Optimal Neural Architectures for Biological Foundation Models Yi Fang H. Xu Jiaxin Han Sirui Ding Y. Wang Yue Wang Xuan Wang LM&Ro AI4CE 201 0 0 29 Nov 2025
Learning from B Cell Evolution: Adaptive Multi-Expert Diffusion for Antibody Design via Online Optimization Hanqi Feng Peng Qiu Mengchun Zhang Yiran Tao You Fan Jingtao Xu Barnabas Poczos DiffM 138 2 0 25 Jul 2025
ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions Matan Halfon Tomer Cohen Raanan Fattal D. Schneidman-Duhovny 159 0 0 26 Jun 2024
Kirigami: large convolutional kernels improve deep learning-based RNA secondary structure prediction Marc Harary Chengxin Zhang 173 0 0 04 Jun 2024
MATE-Pred: Multimodal Attention-based TCR-Epitope interaction PredictorbioRxiv (bioRxiv), 2023 Etienne Goffinet Raghvendra Mall Ankita Singh Rahul Kaushik Filippo Castiglione 161 1 0 05 Dec 2023
OpenProteinSet: Training data for structural biology at scaleNeural Information Processing Systems (NeurIPS), 2023 Gustaf Ahdritz N. Bouatta S. Kadyan Lukas Jarosch Daniel Berenberg Ian Fisk Andrew Watkins Stephen Ra Richard Bonneau Mohammed AlQuraishi AI4CE 189 21 0 10 Aug 2023
MeLM, a generative pretrained language modeling framework that solves forward and inverse mechanics problemsJournal of the mechanics and physics of solids (JMPS), 2023 Markus J. Buehler AI4CE 191 58 0 30 Jun 2023
Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction Jiaxian Yan Zhaofeng Ye Ziyi Yang Chengqiang Lu Shengyu Zhang Qi Liu J. Qiu 159 20 0 08 Jun 2023
Improving Protein-peptide Interface Predictions in the Low Data Regime Justin S. Diamond M. Lill ViT 96 0 0 31 May 2023
Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel ProteinsJournal of Applied Physics (JAP), 2023 Markus J. Buehler 142 26 0 07 May 2023
CoGANPPIS: A Coevolution-enhanced Global Attention Neural Network for Protein-Protein Interaction Site Prediction Jiaxing Guo Xuening Zhu Zixin Hu Xiaoxi Hu 226 0 0 13 Mar 2023
Multimodal Data Integration for Oncology in the Era of Deep Neural Networks: A Review Asim Waqas Aakash Tripathi Ravichandran Ramachandran Paul Stewart Ghulam Rasool AI4CE 381 72 0 11 Mar 2023
Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching PerspectiveInternational Conference on Machine Learning (ICML), 2022 Cheng Tan Zhangyang Gao Hanqun Cao Xingran Chen Ge Wang Lirong Wu Jun Xia Jiangbin Zheng Stan Z. Li 235 2 0 02 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 198 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 190 45 0 30 Nov 2022
Diffusion-based Molecule Generation with Informative Prior BridgesNeural Information Processing Systems (NeurIPS), 2022 Lemeng Wu Chengyue Gong Xingchao Liu Mao Ye Qiang Liu DiffM 262 139 0 02 Sep 2022
PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction Sirui Liu Jun Zhang Haotian Chu Min Wang Boxin Xue ... Zidong Wang Lijiang Yang Fan Yu Lei Chen Y. Gao 3DV 183 15 0 24 Jun 2022
Exploring evolution-aware & -free protein language models as protein function predictorsNeural Information Processing Systems (NeurIPS), 2022 Min Hu Fajie Yuan Kevin Kaichuang Yang Fusong Ju Jingyu Su Hongya Wang Fei Yang Qiuyang Ding 223 53 0 14 Jun 2022
Symmetry Structured Convolutional Neural Networks K. D. G. Maduranga Vasily Zadorozhnyy Qiang Ye 163 6 0 03 Mar 2022
HRel: Filter Pruning based on High Relevance between Activation Maps and Class LabelsNeural Networks (NN), 2021 C. Sarvani Mrinmoy Ghorai S. Dubey S. H. Shabbeer Basha VLM 258 45 0 22 Feb 2022
Learning to Discover MedicinesInternational Journal of Data Science and Analysis (JDSA), 2022 T. Nguyen Thin Nguyen T. Tran 162 2 0 14 Feb 2022
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 Jia Zhang Tao Qin Tie-Yan Liu 187 35 0 29 Oct 2021
Protein-RNA interaction prediction with deep learning: Structure matters Junkang Wei Siyuan Chen Licheng Zong Xin Gao Yu Li AI4CE 183 72 0 26 Jul 2021
G-VAE, a Geometric Convolutional VAE for ProteinStructure Generation Niraj Pudasaini Boulbaba Ben Amor Xichan Lin Fan Zhu Yi Fang DRL 102 7 0 22 Jun 2021
Protein sequence-to-structure learning: Is this the end(-to-end revolution)?Proteins: Structure, Function, and Bioinformatics (Proteins), 2021 É. Laine Stephan Eismann A. Elofsson Sergei Grudinin OOD 3DV 191 37 0 16 May 2021
tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modeling Structure Refinement Liangzhen Zheng Haidong Lan Tao Shen Jiaxiang Wu Sheng Wang Wei Liu Junzhou Huang 283 1 0 10 May 2021
Which transformer architecture fits my data? A vocabulary bottleneck in self-attentionInternational Conference on Machine Learning (ICML), 2021 Noam Wies Yoav Levine Daniel Jannai Amnon Shashua 176 22 0 09 May 2021
Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance ComputersInterface Focus (IF), 2021 Agastya P. Bhati S. Wan Dario Alfè Austin R. Clyde Mathis Bode ... A. Partin Fangfang Xia Xiaotan Duan Rick L. Stevens P. V. Coveney 175 28 0 04 Mar 2021
Deep Multi-attribute Graph Representation Learning on Protein Structures Tian Xia Wei-Shinn Ku GNN AI4CE 177 2 0 22 Dec 2020
Cross-Modality Protein Embedding for Compound-Protein Affinity and Contact PredictionbioRxiv (bioRxiv), 2020 Yuning You Yang Shen 164 8 0 14 Nov 2020
Decoy Selection for Protein Structure Prediction Via Extreme Gradient Boosting and RankingBMC Bioinformatics (BB), 2020 N. Akhter Gopinath Chennupati H. Djidjev Amarda Shehu 81 5 0 03 Oct 2020
GEFA: Early Fusion Approach in Drug-Target Affinity PredictionIEEE/ACM Transactions on Computational Biology & Bioinformatics (TCBB), 2020 T. Nguyen Thin Nguyen T. Le T. Tran GNN 188 69 0 25 Sep 2020
Unsupervised and Supervised Structure Learning for Protein Contact Prediction S. Sun 128 0 0 31 Aug 2020
Towards Structured Prediction in Bioinformatics with Deep Learning Yu Li AI4CE 124 1 0 25 Aug 2020
Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing V. Ioannidis Da Zheng George Karypis 132 52 0 20 Jul 2020
Deep Learning in Protein Structural Modeling and Design Wenhao Gao S. Mahajan Jeremias Sulam Jeffrey J. Gray 173 179 0 16 Jul 2020
The prospects of quantum computing in computational molecular biology C. Outeiral M. Strahm Jiye Shi Garrett M. Morris S. Benjamin Charlotte M. Deane 166 205 0 26 May 2020
Generating Tertiary Protein Structures via an Interpretative Variational Autoencoder Xiaojie Guo Yuanqi Du Sivani Tadepalli Bo Pan Amarda Shehu DRL 138 28 0 08 Apr 2020
RNA Secondary Structure Prediction By Learning Unrolled AlgorithmsInternational Conference on Learning Representations (ICLR), 2020 Xinshi Chen Yu Li Ramzan Umarov Xin Gao Le Song SyDa AI4TS 104 129 0 13 Feb 2020
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and ContactsbioRxiv (bioRxiv), 2019 Mostafa Karimi Di Wu Zinan Lin Yang Shen 207 51 0 29 Dec 2019
Machine learning for protein folding and dynamicsCurrent Opinion in Structural Biology (Curr. Opin. Struct. Biol.), 2019 Frank Noé Gianni De Fabritiis C. Clementi AI4CE 153 146 0 22 Nov 2019
Universal Transforming Geometric Network Jin Li 222 9 0 02 Aug 2019
Towards Compact and Robust Deep Neural Networks Vikash Sehwag Shiqi Wang Prateek Mittal Suman Jana AAML 125 41 0 14 Jun 2019
ImJoy: an open-source computational platform for the deep learning eraNature Methods (Nat. Methods), 2019 Ouyang Wei F. Mueller Martin Hjelmare E. Lundberg C. Zimmer VLM AI4CE 165 125 0 30 May 2019
Deep learning in bioinformatics: introduction, application, and perspective in big data erabioRxiv (bioRxiv), 2019 Yu Li Chao Huang Lizhong Ding Zhongxiao Li Yijie Pan Xin Gao AI4CE 217 320 0 28 Feb 2019
Learning protein sequence embeddings using information from structure Tristan Bepler Bonnie Berger 214 316 0 22 Feb 2019
DeepSymmetry : Using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures Guillaume Pagès Sergei Grudinin 141 9 0 29 Oct 2018
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning Haicang Zhang Qi Zhang Fusong Ju Jianwei Zhu Shiwei Sun ... Ziwei Xie Minghua Deng Shiwei Sun Weinan Zheng Dongbo Bu 110 9 0 31 Aug 2018
Dihedral angle prediction using generative adversarial networks Hyeongki Kim GAN 244 0 0 29 Mar 2018
Deep Learning for Genomics: A Concise Overview Tianwei Yue Yuanxin Wang Longxiang Zhang Chunming Gu Haohan Wang Wenping Wang Qi Lyu Yujie Dun AILaw VLM BDL 245 96 0 02 Feb 2018