Sheng-You Huang

43 papers Journal 42Unranked 1

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	A Robust and Efficient Multi-Agent Reinforcement Learning Framework for Traffic Signal Control. CoRR Sheng-You Huang, Hsiao-Chuan Chang, Yen-Chi Chen, Ting-Han Wei, I-Hau Yeh, Sheng-Yao Kuan, Chien-Yao Wang, Hsuan-Han Lee, I-Chen Wu
2026	J	`jnl`	VissimRL: A Multi-Agent Reinforcement Learning Framework for Traffic Signal Control Based on Vissim. CoRR Hsiao-Chuan Chang, Sheng-You Huang, Yen-Chi Chen, I-Chen Wu
2025	J	`jnl`	Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning. J. Chem. Inf. Model. Hong Cao, Jiahua He, Tao Li, Sheng-You Huang
2025	J	`jnl`	Improved Prediction of Drug-Protein Interactions through Physics-Based Few-Shot Learning. J. Chem. Inf. Model. Keqiong Zhang, Zhiran Fan, Qilong Wu, Jianfeng Liu, Sheng-You Huang
2024	J	`jnl`	XDock: A General Docking Method for Modeling Protein-Ligand and Nucleic Acid-Ligand Interactions. J. Chem. Inf. Model. Qilong Wu, Sheng-You Huang
2023	J	`jnl`	DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning. Briefings Bioinform. Peicong Lin, Yumeng Yan, Sheng-You Huang
2023	J	`jnl`	HCovDock: an efficient docking method for modeling covalent protein-ligand interactions. Briefings Bioinform. Qilong Wu, Sheng-You Huang
2023	J	`jnl`	Protein-protein contact prediction by geometric triangle-aware protein language models. Nat. Mac. Intell. Peicong Lin, Huanyu Tao, Hao Li, Sheng-You Huang
2022	J	`jnl`	Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy. Bioinform. Huanyu Tao, Xuejun Zhao, Keqiong Zhang, Peicong Lin, Sheng-You Huang
2022	J	`jnl`	Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. J. Cheminformatics Huanyu Tao, Qilong Wu, Xuejun Zhao, Peicong Lin, Sheng-You Huang
2022	J	`jnl`	Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. J. Chem. Inf. Model. Jinze Zhang, Hao Li, Xuejun Zhao, Qilong Wu, Sheng-You Huang
2022	J	`jnl`	Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials. J. Chem. Inf. Model. Hao Li, Yumeng Yan, Xuejun Zhao, Sheng-You Huang
2022	J	`jnl`	TRScore: a 3D RepVGG-based scoring method for ranking protein docking models. Bioinform. Linyuan Guo, Jiahua He, Peicong Lin, Sheng-You Huang, Jianxin Wang
2021	J	`jnl`	Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes. Briefings Bioinform. Yumeng Yan, Sheng-You Huang
2021	J	`jnl`	EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps. Briefings Bioinform. Jiahua He, Sheng-You Huang
2021	J	`jnl`	Full-length de novo protein structure determination from cryo-EM maps using deep learning. Bioinform. Jiahua He, Sheng-You Huang
2021	J	`jnl`	NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes. J. Chem. Inf. Model. Yuyu Feng, Keqiong Zhang, Qilong Wu, Sheng-You Huang
2020	J	`jnl`	ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid-Ligand Interactions. J. Chem. Inf. Model. Yuyu Feng, Sheng-You Huang
2020	J	`jnl`	Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. J. Chem. Inf. Model. Huanyu Tao, Yanjun Zhang, Sheng-You Huang
2020	J	`jnl`	Topology-independent and global protein structure alignment through an FFT-based algorithm. Bioinform. Zeyu Wen, Jiahua He, Sheng-You Huang
2019	J	`jnl`	A non-redundant benchmark for symmetric protein docking. Big Data Min. Anal. Yumeng Yan, Sheng-You Huang
2019	J	`jnl`	HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. Nucleic Acids Res. Jiahua He, Jun Wang, Huanyu Tao, Yi Xiao, Sheng-You Huang
2019	J	`jnl`	Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction. J. Chem. Inf. Model. Xinxiang Wang, Sheng-You Huang
2019	J	`jnl`	PepBDB: a comprehensive structural database of biological peptide-protein interactions. Bioinform. Zeyu Wen, Jiahua He, Huanyu Tao, Sheng-You Huang
2019	J	`jnl`	Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. Bioinform. Jiahua He, Huanyu Tao, Sheng-You Huang
2019	J	`jnl`	Pushing the accuracy limit of shape complementarity for protein-protein docking. BMC Bioinform. Yumeng Yan, Sheng-You Huang
2018	J	`jnl`	Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges. Briefings Bioinform. Sheng-You Huang
2018	J	`jnl`	HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Res. Pei Zhou, Bowen Jin, Hao Li, Sheng-You Huang
2018	J	`jnl`	HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. Nucleic Acids Res. Yumeng Yan, Huanyu Tao, Sheng-You Huang
2018	J	`jnl`	Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. J. Chem. Inf. Model. Pei Zhou, Botong Li, Yumeng Yan, Bowen Jin, Libang Wang, Sheng-You Huang
2018	J	`jnl`	New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. J. Chem. Inf. Model. Xinxiang Wang, Di Zhang, Sheng-You Huang
2018	—	`conf`	Protein-Protein Docking with Improved Shape Complementarity. ICIC (1) Yumeng Yan, Sheng-You Huang
2018	J	`jnl`	RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. Bioinform. Yumeng Yan, Sheng-You Huang
2017	J	`jnl`	Efficient conformational ensemble generation of protein-bound peptides. J. Cheminformatics Yumeng Yan, Di Zhang, Sheng-You Huang
2017	J	`jnl`	HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res. Yumeng Yan, Di Zhang, Pei Zhou, Botong Li, Sheng-You Huang
2016	J	`jnl`	HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches. J. Chem. Inf. Model. Sheng-You Huang, Min Li, Jianxin Wang, Yi Pan
2013	J	`jnl`	A nonredundant structure dataset for benchmarking protein-RNA computational docking. J. Comput. Chem. Sheng-You Huang, Xiaoqin Zou
2013	J	`jnl`	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. Sam Z. Grinter, Chengfei Yan, Sheng-You Huang, Lin Jiang, Xiaoqin Zou
2011	J	`jnl`	Construction and Test of Ligand Decoy Sets Using MDock: Community Structure-Activity Resource Benchmarks for Binding Mode Prediction. J. Chem. Inf. Model. Sheng-You Huang, Xiaoqin Zou
2011	J	`jnl`	Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function. J. Chem. Inf. Model. Sheng-You Huang, Xiaoqin Zou
2010	J	`jnl`	Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions. J. Chem. Inf. Model. Sheng-You Huang, Xiaoqin Zou
2006	J	`jnl`	An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J. Comput. Chem. Sheng-You Huang, Xiaoqin Zou
2006	J	`jnl`	An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J. Comput. Chem. Sheng-You Huang, Xiaoqin Zou