Sheng-You Huang

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 30

Top Topics

Experimentally Determined

Protein Interaction

Scoring Function

Protein Structure

Top Venues

J. Chem. Inf. Model.

Briefings Bioinform.

Nucleic Acids Res.

Publications

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) (2023)
Qilong Wu, Sheng-You Huang
HCovDock: an efficient docking method for modeling covalent protein-ligand interactions. Briefings Bioinform. 24 (1) (2023)
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)
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) (2022)
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) (2022)
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) (2022)
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) (2022)
Jiahua He, Sheng-You Huang
EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps. Briefings Bioinform. 22 (6) (2021)
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) (2021)
Jiahua He, Sheng-You Huang
Full-length de novo protein structure determination from cryo-EM maps using deep learning. Bioinform. 37 (20) (2021)
Yumeng Yan, Sheng-You Huang
Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes. Briefings Bioinform. 22 (5) (2021)
Zeyu Wen, Jiahua He, Sheng-You Huang
Topology-independent and global protein structure alignment through an FFT-based algorithm. Bioinform. 36 (2) (2020)
Yuyu Feng, Sheng-You Huang
ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid-Ligand Interactions. J. Chem. Inf. Model. 60 (12) (2020)
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) (2020)
Jiahua He, Huanyu Tao, Sheng-You Huang
Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. Bioinform. 35 (23) (2019)
Yumeng Yan, Sheng-You Huang
Pushing the accuracy limit of shape complementarity for protein-protein docking. BMC Bioinform. (25) (2019)
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) (2019)
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) (2019)
Yumeng Yan, Sheng-You Huang
A non-redundant benchmark for symmetric protein docking. Big Data Min. Anal. 2 (2) (2019)
Zeyu Wen, Jiahua He, Huanyu Tao, Sheng-You Huang
PepBDB: a comprehensive structural database of biological peptide-protein interactions. Bioinform. 35 (1) (2019)
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) (2018)
Yumeng Yan, Sheng-You Huang
Protein-Protein Docking with Improved Shape Complementarity. ICIC (1) (2018)
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) (2018)
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) (2018)
Sheng-You Huang
Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges. Briefings Bioinform. 19 (5) (2018)
Yumeng Yan, Sheng-You Huang
RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. Bioinform. 34 (3) (2018)
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) (2018)
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) (2017)
Yumeng Yan, Di Zhang, Sheng-You Huang
Efficient conformational ensemble generation of protein-bound peptides. J. Cheminformatics 9 (1) (2017)
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) (2016)
Sheng-You Huang, Xiaoqin Zou
A nonredundant structure dataset for benchmarking protein-RNA computational docking. J. Comput. Chem. 34 (4) (2013)
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) (2013)
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) (2011)
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) (2011)
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) (2010)
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) (2006)
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) (2006)