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Journal Articles
- 2023
[j36]Peicong Lin, Yumeng Yan, Sheng-You Huang:
DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning. Briefings Bioinform. 24(1) (2023)- [j35]Qilong Wu, Sheng-You Huang:
HCovDock: an efficient docking method for modeling covalent protein-ligand interactions. Briefings Bioinform. 24(1) (2023) - [j34]Peicong Lin, Huanyu Tao, Hao Li, Sheng-You Huang
:
Protein-protein contact prediction by geometric triangle-aware protein language models. Nat. Mac. Intell. 5(11): 1275-1284 (2023) - 2022
- [j33]Huanyu Tao, Xuejun Zhao, Keqiong Zhang, Peicong Lin, Sheng-You Huang:
Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy. Bioinform. 38(17): 4109-4116 (2022) - [j32]Huanyu Tao, Qilong Wu, Xuejun Zhao, Peicong Lin, Sheng-You Huang:
Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. J. Cheminformatics 14(1): 26 (2022) - [j31]Hao Li, Yumeng Yan, Xuejun Zhao, Sheng-You Huang:
Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials. J. Chem. Inf. Model. 62(3): 740-750 (2022) - [j30]Jinze Zhang, Hao Li, Xuejun Zhao, Qilong Wu, Sheng-You Huang:
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. J. Chem. Inf. Model. 62(22): 5806-5820 (2022) - 2021
- [j29]Yumeng Yan, Sheng-You Huang:
Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes. Briefings Bioinform. 22(5) (2021) - [j28]Jiahua He, Sheng-You Huang:
EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps. Briefings Bioinform. 22(6) (2021) - [j27]Jiahua He, Sheng-You Huang:
Full-length de novo protein structure determination from cryo-EM maps using deep learning. Bioinform. 37(20): 3480-3490 (2021) - [j26]Yuyu Feng, Keqiong Zhang, Qilong Wu, Sheng-You Huang:
NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes. J. Chem. Inf. Model. 61(9): 4771-4782 (2021) - 2020
- [j25]Zeyu Wen, Jiahua He, Sheng-You Huang:
Topology-independent and global protein structure alignment through an FFT-based algorithm. Bioinform. 36(2): 478-486 (2020) - [j24]Huanyu Tao, Yanjun Zhang, Sheng-You Huang:
Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. J. Chem. Inf. Model. 60(4): 2377-2387 (2020) - [j23]Yuyu Feng, Sheng-You Huang:
ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid-Ligand Interactions. J. Chem. Inf. Model. 60(12): 6698-6708 (2020) - 2019
- [j22]Yumeng Yan, Sheng-You Huang:
A non-redundant benchmark for symmetric protein docking. Big Data Min. Anal. 2(2): 92-99 (2019) - [j21]Zeyu Wen, Jiahua He, Huanyu Tao, Sheng-You Huang:
PepBDB: a comprehensive structural database of biological peptide-protein interactions. Bioinform. 35(1): 175-177 (2019) - [j20]Jiahua He, Huanyu Tao, Sheng-You Huang:
Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. Bioinform. 35(23): 4994-5002 (2019) - [j19]Yumeng Yan, Sheng-You Huang:
Pushing the accuracy limit of shape complementarity for protein-protein docking. BMC Bioinform. 20-S(25): 696 (2019) - [j18]Xinxiang Wang, Sheng-You Huang:
Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction. J. Chem. Inf. Model. 59(6): 3080-3090 (2019) - [j17]Jiahua He, Jun Wang, Huanyu Tao, Yi Xiao, Sheng-You Huang:
HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. Nucleic Acids Res. 47(Webserver-Issue): W35-W42 (2019) - 2018
- [j16]Sheng-You Huang:
Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges. Briefings Bioinform. 19(5): 982-994 (2018) - [j15]Yumeng Yan, Sheng-You Huang:
RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. Bioinform. 34(3): 453-458 (2018) - [j14]Xinxiang Wang, Di Zhang, Sheng-You Huang:
New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. J. Chem. Inf. Model. 58(3): 724-732 (2018) - [j13]Pei Zhou, Botong Li, Yumeng Yan, Bowen Jin, Libang Wang, Sheng-You Huang:
Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. J. Chem. Inf. Model. 58(6): 1292-1302 (2018) - [j12]Yumeng Yan, Huanyu Tao, Sheng-You Huang:
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. Nucleic Acids Res. 46(Webserver-Issue): W423-W431 (2018) - [j11]Pei Zhou, Bowen Jin, Hao Li, Sheng-You Huang:
HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Res. 46(Webserver-Issue): W443-W450 (2018) - 2017
- [j10]Yumeng Yan, Di Zhang, Sheng-You Huang:
Efficient conformational ensemble generation of protein-bound peptides. J. Cheminformatics 9(1): 59:1-59:13 (2017) - [j9]Yumeng Yan, Di Zhang, Pei Zhou, Botong Li, Sheng-You Huang:
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res. 45(Webserver-Issue): W365-W373 (2017) - 2016
- [j8]Sheng-You Huang, Min Li, Jianxin Wang, Yi Pan:
HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches. J. Chem. Inf. Model. 56(6): 1078-1087 (2016) - 2013
- [j7]Sheng-You Huang, Xiaoqin Zou:
A nonredundant structure dataset for benchmarking protein-RNA computational docking. J. Comput. Chem. 34(4): 311-318 (2013) - [j6]Sam Z. Grinter, Chengfei Yan, Sheng-You Huang, Lin Jiang, Xiaoqin Zou:
Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure-Activity Resource Benchmark. J. Chem. Inf. Model. 53(8): 1905-1914 (2013) - 2011
- [j5]Sheng-You Huang, Xiaoqin Zou:
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function. J. Chem. Inf. Model. 51(9): 2097-2106 (2011) - [j4]Sheng-You Huang, Xiaoqin Zou:
Construction and Test of Ligand Decoy Sets Using MDock: Community Structure-Activity Resource Benchmarks for Binding Mode Prediction. J. Chem. Inf. Model. 51(9): 2107-2114 (2011) - 2010
- [j3]Sheng-You Huang, Xiaoqin Zou:
Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions. J. Chem. Inf. Model. 50(2): 262-273 (2010) - 2006
- [j2]Sheng-You Huang, Xiaoqin Zou:
An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J. Comput. Chem. 27(15): 1866-1875 (2006) - [j1]Sheng-You Huang, Xiaoqin Zou:
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J. Comput. Chem. 27(15): 1876-1882 (2006)
Conference and Workshop Papers
- 2018
- [c1]Yumeng Yan, Sheng-You Huang:
Protein-Protein Docking with Improved Shape Complementarity. ICIC (1) 2018: 600-605
Coauthor Index
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