An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. - Sheng-You Huang; Xiaoqin Zou (J. Comput. Chem., 2006)

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. - Sheng-You Huang; Xiaoqin Zou (J. Comput. Chem., 2006)

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions. - Sheng-You Huang; Xiaoqin Zou (J. Chem. Inf. Model., 2010)

Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function. - Sheng-You Huang; Xiaoqin Zou (J. Chem. Inf. Model., 2011)

Construction and Test of Ligand Decoy Sets Using MDock: Community Structure-Activity Resource Benchmarks for Binding Mode Prediction. - Sheng-You Huang; Xiaoqin Zou (J. Chem. Inf. Model., 2011)

A nonredundant structure dataset for benchmarking protein-RNA computational docking. - Sheng-You Huang; Xiaoqin Zou (J. Comput. Chem., 2013)

Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure-Activity Resource Benchmark. - Sam Z. Grinter; Chengfei Yan; Sheng-You Huang; Lin Jiang; Xiaoqin Zou (J. Chem. Inf. Model., 2013)

HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches. - Sheng-You Huang; Min Li 007; Jianxin Wang 001; Yi Pan 001 (J. Chem. Inf. Model., 2016)

Efficient conformational ensemble generation of protein-bound peptides. - Yumeng Yan; Di Zhang; Sheng-You Huang (J. Cheminformatics, 2017)

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. - Yumeng Yan; Di Zhang; Pei Zhou; Botong Li; Sheng-You Huang (Nucleic Acids Res., 2017)

Protein-Protein Docking with Improved Shape Complementarity. - Yumeng Yan; Sheng-You Huang (ICIC (1), 2018)

Comprehensive assessment of flexible-ligand docking algorithms: current effectiveness and challenges. - Sheng-You Huang (Briefings Bioinform., 2018)

RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring. - Yumeng Yan; Sheng-You Huang (Bioinform., 2018)

New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. - Xinxiang Wang; Di Zhang; Sheng-You Huang (J. Chem. Inf. Model., 2018)

Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. - Pei Zhou; Botong Li; Yumeng Yan; Bowen Jin; Libang Wang; Sheng-You Huang (J. Chem. Inf. Model., 2018)

HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry. - Yumeng Yan; Huanyu Tao; Sheng-You Huang (Nucleic Acids Res., 2018)

HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm. - Pei Zhou; Bowen Jin; Hao Li; Sheng-You Huang (Nucleic Acids Res., 2018)

A non-redundant benchmark for symmetric protein docking. - Yumeng Yan; Sheng-You Huang (Big Data Min. Anal., 2019)

Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models. - Jiahua He; Huanyu Tao; Sheng-You Huang (Bioinform., 2019)

PepBDB: a comprehensive structural database of biological peptide-protein interactions. - Zeyu Wen; Jiahua He; Huanyu Tao; Sheng-You Huang (Bioinform., 2019)

Pushing the accuracy limit of shape complementarity for protein-protein docking. - Yumeng Yan; Sheng-You Huang (BMC Bioinform., 2019)

Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction. - Xinxiang Wang; Sheng-You Huang (J. Chem. Inf. Model., 2019)

HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures. - Jiahua He; Jun Wang; Huanyu Tao; Yi Xiao; Sheng-You Huang (Nucleic Acids Res., 2019)

Topology-independent and global protein structure alignment through an FFT-based algorithm. - Zeyu Wen; Jiahua He; Sheng-You Huang (Bioinform., 2020)

ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid-Ligand Interactions. - Yuyu Feng 002; Sheng-You Huang (J. Chem. Inf. Model., 2020)

Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. - Huanyu Tao; Yanjun Zhang; Sheng-You Huang (J. Chem. Inf. Model., 2020)

EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps. - Jiahua He; Sheng-You Huang (Briefings Bioinform., 2021)

Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes. - Yumeng Yan; Sheng-You Huang (Briefings Bioinform., 2021)

Full-length de novo protein structure determination from cryo-EM maps using deep learning. - Jiahua He; Sheng-You Huang (Bioinform., 2021)

NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes. - Yuyu Feng 002; Keqiong Zhang; Qilong Wu 001; Sheng-You Huang (J. Chem. Inf. Model., 2021)

TRScore: a 3D RepVGG-based scoring method for ranking protein docking models. - Linyuan Guo; Jiahua He; Peicong Lin; Sheng-You Huang; Jianxin Wang 001 (Bioinform., 2022)

Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy. - Huanyu Tao; Xuejun Zhao; Keqiong Zhang; Peicong Lin; Sheng-You Huang (Bioinform., 2022)

Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. - Huanyu Tao; Qilong Wu 001; Xuejun Zhao; Peicong Lin; Sheng-You Huang (J. Cheminformatics, 2022)

Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials. - Hao Li; Yumeng Yan; Xuejun Zhao; Sheng-You Huang (J. Chem. Inf. Model., 2022)

Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. - Jinze Zhang; Hao Li; Xuejun Zhao; Qilong Wu 001; Sheng-You Huang (J. Chem. Inf. Model., 2022)

DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning. - Peicong Lin; Yumeng Yan; Sheng-You Huang (Briefings Bioinform., 2023)

HCovDock: an efficient docking method for modeling covalent protein-ligand interactions. - Qilong Wu 001; Sheng-You Huang (Briefings Bioinform., 2023)

Protein-protein contact prediction by geometric triangle-aware protein language models. - Peicong Lin; Huanyu Tao; Hao Li; Sheng-You Huang (Nat. Mac. Intell., 2023)

XDock: A General Docking Method for Modeling Protein-Ligand and Nucleic Acid-Ligand Interactions. - Qilong Wu 001; Sheng-You Huang (J. Chem. Inf. Model., 2024)

Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning. - Hong Cao; Jiahua He; Tao Li; Sheng-You Huang (J. Chem. Inf. Model., 2025)

Improved Prediction of Drug-Protein Interactions through Physics-Based Few-Shot Learning. - Keqiong Zhang; Zhiran Fan; Qilong Wu 001; Jianfeng Liu; Sheng-You Huang (J. Chem. Inf. Model., 2025)