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Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials 期刊论文
COMMUNICATIONS BIOLOGY, 2024, 卷号: 7, 期号: 1, 页码: 13
作者:  Gong, Tiansu;  Ju, Fusong;  Bu, Dongbo
收藏  |  浏览/下载:3/0  |  提交时间:2024/05/20
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:6/0  |  提交时间:2024/05/20
Deep learning  protein structure prediction  
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:18/0  |  提交时间:2022/12/07
deep learning and protein threading  protein alignment  protein structure prediction  
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 期号: 1, 页码: 11
作者:  Zhang, Haicang;  Zhang, Qi;  Ju, Fusong;  Zhu, Jianwei;  Gao, Yujuan;  Xie, Ziwei;  Deng, Minghua;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载:46/0  |  提交时间:2020/12/10
Residue-residue contacts prediction  Deep learning  Markov random fields  Composite likelihood maximization  
Constrained maximum weighted bipartite matching: a novel approach to radio broadcast scheduling 期刊论文
SCIENCE CHINA-INFORMATION SCIENCES, 2019, 卷号: 62, 期号: 7, 页码: 14
作者:  Wang, Shaojiang;  Wu, Tianyong;  Yao, Yuan;  Bu, Dongbo;  Cai, Shaowei
收藏  |  浏览/下载:85/0  |  提交时间:2019/08/16
radio broadcast scheduling  branch-and-bound algorithm  constrained maximum weighted bipartite matching  Kuhn-Munkres algorithm  strategy combinations  
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:80/0  |  提交时间:2019/08/16
Protein structure prediction  Energy function  Attraction-basin  Reverse Monte Carlo sampling  Monte Carlo search  Linear program  
Genome-wide analysis of mammalian DNA segment fusion/fission 期刊论文
JOURNAL OF THEORETICAL BIOLOGY, 2006, 卷号: 240, 期号: 2, 页码: 200-208
作者:  Zhang, Zhihua;  Sun, Hong;  Zhang, Yong;  Zhao, Yi;  Shi, Baochen;  Sun, Shiwei;  Lu, Hongchao;  Bu, Dongbo;  Ling, Lunjiang;  Chen, Runsheng
收藏  |  浏览/下载:37/0  |  提交时间:2019/12/16
fusion  fission  mammalian comparative genomic  non-protein coding DNA segment