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Single-sequence protein structure prediction by integrating protein language models 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2024, 卷号: 121, 期号: 13, 页码: 7
作者:  Jing, Xiaoyang;  Wu, Fandi;  Luo, Xiao;  Xu, Jinbo
收藏  |  浏览/下载：6/0  |  提交时间：2024/05/20
protein structure prediction  protein language model  single-sequence protein structure rediction  antibody structure prediction  single mutation effect  
SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances 期刊论文
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2023, 卷号: 20, 期号: 6, 页码: 3482-3488
作者:  Gong, Tiansu;  Ju, Fusong;  Sun, Shiwei;  Bu, Dongbo
收藏  |  浏览/下载：18/0  |  提交时间：2024/05/20
Deep learning  protein structure prediction  
Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms 期刊论文
GENOMICS PROTEOMICS & BIOINFORMATICS, 2023, 卷号: 21, 期号: 5, 页码: 913-925
作者:  Huang, Bin;  Kong, Lupeng;  Wang, Chao;  Ju, Fusong;  Zhang, Qi;  Zhu, Jianwei;  Gong, Tiansu;  Zhang, Haicang;  Yu, Chungong;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载：6/0  |  提交时间：2024/05/20
Protein folding  Protein structure prediction  Deep learning  Transformer  Language model  
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs 期刊论文
JOURNAL OF COMPUTATIONAL BIOLOGY, 2022, 页码: 14
作者:  Kong, Lupeng;  Ju, Fusong;  Zheng, Wei-mou;  Zhu, Jianwei;  Sun, Shiwei;  Xu, Jinbo;  Bu, Dongbo
收藏  |  浏览/下载：23/0  |  提交时间：2022/12/07
deep learning and protein threading  protein alignment  protein structure prediction  
FALCON2: a web server for high-quality prediction of protein tertiary structures 期刊论文
BMC BIOINFORMATICS, 2021, 卷号: 22, 期号: 1, 页码: 14
作者:  Kong, Lupeng;  Ju, Fusong;  Zhang, Haicang;  Sun, Shiwei;  Bu, Dongbo
收藏  |  浏览/下载：42/0  |  提交时间：2021/12/01
Protein structure prediction  Template-based modeling  Ab initio prediction  Protein structure prediction web service  
Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 页码: 10
作者:  Wang, Chao;  Wei, Yi;  Zhang, Haicang;  Kong, Lupeng;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载：86/0  |  提交时间：2019/08/16
Protein structure prediction  Energy function  Attraction-basin  Reverse Monte Carlo sampling  Monte Carlo search  Linear program  
COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming 期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016, 卷号: 84, 期号: 3, 页码: 332-348
作者:  Zhang, Huiling;  Huang, Qingsheng;  Bei, Zhendong;  Wei, Yanjie;  Floudas, Christodoulos A.
收藏  |  浏览/下载：44/0  |  提交时间：2019/12/13
protein structure prediction  hybrid framework  machine learning  ab initio prediction  MILP  
Fragment-HMM: A new approach to protein structure prediction 期刊论文
PROTEIN SCIENCE, 2008, 卷号: 17, 期号: 11, 页码: 1925-1934
作者:  Li, Shuai Cheng;  Bu, Dongbo;  Xu, Jinbo;  Li, Ming
收藏  |  浏览/下载：45/0  |  提交时间：2019/12/16
protein structure prediction  hidden Markov model  fragment assembly