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GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states 期刊论文
BMC BIOINFORMATICS, 2024, 卷号: 25, 期号: 1, 页码: 16
作者:  Liu, Fan;  Zhou, Han;  Li, Xiaonong;  Zhou, Liangliang;  Yu, Chungong;  Zhang, Haicang;  Bu, Dongbo;  Liang, Xinmiao
收藏  |  浏览/下载：1/0  |  提交时间：2024/12/06
G-protein coupled receptor  State-specific structure  Binding site  Key residue  Database  
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：10/0  |  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：34/0  |  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：10/0  |  提交时间：2024/05/20
Protein folding  Protein structure prediction  Deep learning  Transformer  Language model  
Recent Progress in Chemical Cross-linking Coupled With Mass Spectrometry 期刊论文
PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 2022, 卷号: 49, 期号: 4, 页码: 737-758
作者:  Chen Zhen-Lin;  Cao Yong;  He Si-Min
收藏  |  浏览/下载：29/0  |  提交时间：2022/12/07
cross-linking mass spectrometry  protein structure  protein interaction  proteomics  mass spectrometry  
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：26/0  |  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：46/0  |  提交时间：2021/12/01
Protein structure prediction  Template-based modeling  Ab initio prediction  Protein structure prediction web service  
ISSEC: inferring contacts among protein secondary structure elements using deep object detection 期刊论文
BMC BIOINFORMATICS, 2020, 卷号: 21, 期号: 1, 页码: 13
作者:  Zhang, Qi;  Zhu, Jianwei;  Ju, Fusong;  Kong, Lupeng;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载：37/0  |  提交时间：2021/12/01
Protein structure  Secondary structure elements  Inter-SSE contacts  
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：90/0  |  提交时间：2019/08/16
Protein structure prediction  Energy function  Attraction-basin  Reverse Monte Carlo sampling  Monte Carlo search  Linear program  
Improving prediction of burial state of residues by exploiting correlation among residues 期刊论文
BMC BIOINFORMATICS, 2017, 卷号: 18, 页码: 11
作者:  Gong, Hai'e;  Zhang, Haicang;  Zhu, Jianwei;  Wang, Chao;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
收藏  |  浏览/下载：64/0  |  提交时间：2019/12/12
Protein structure  Burial states of residue  Conditional random field  Residue correlation