QM/MM study of catalytic methyl transfer by the N5-glutamine SAM-dependent methyltransferase and its inhibition by the nitrogen analogue of coenzyme. - Ruibo Wu; Zexing Cao (J. Comput. Chem., 2008)

Effects of electron attachment on C5'-O5' and C1'-N1 bond cleavages of pyrimidine nucleotides: A theoretical study. - Hujun Xie; Ruibo Wu; Fei Xia; Zexing Cao (J. Comput. Chem., 2008)

Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase. - Xin Zhang 020; Ruibo Wu; Lingchun Song; Yuchun Lin; Menghai Lin; Zexing Cao; Wei Wu 030; Yirong Mo (J. Comput. Chem., 2009)

Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing. - Hu Ge; Yu Wang; Chanjuan Li; Nanhao Chen; Yufang Xie; Mengyan Xu; Yingyan He; Xinchun Gu; Ruibo Wu; Qiong Gu; Liang Zeng; Jun Xu 017 (J. Chem. Inf. Model., 2013)

Structure-Function Analysis of the Conserved Tyrosine and Diverse π-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study. - Jingwei Zhou; Hujun Xie; Zhihong Liu; Hai-Bin Luo; Ruibo Wu (J. Chem. Inf. Model., 2014)

Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study. - Wenjing Gong; Ruibo Wu; Yingkai Zhang (J. Comput. Chem., 2015)

Binding Kinetics versus Affinities in BRD4 Inhibition. - Ming Kuang; Jingwei Zhou; Laiyou Wang; Zhihong Liu; Jiao Guo; Ruibo Wu (J. Chem. Inf. Model., 2015)

Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS. - Fan Zhang; Nanhao Chen; Ruibo Wu (J. Chem. Inf. Model., 2016)

Intrinsic Dynamics of the Binding Rail and Its Allosteric Effect in the Class I Histone Deacetylases. - Jingwei Zhou; Yue Huang; Chunyan Cheng; Kai Wang 063; Ruibo Wu (J. Chem. Inf. Model., 2017)

Exploring Chemical and Biological Space of Terpenoids. - Tao Zeng; Zhihong Liu; Huawei Liu; Wengan He; Xiaowen Tang; Liwei Xie; Ruibo Wu (J. Chem. Inf. Model., 2019)

GM-DockZn: a geometry matching-based docking algorithm for zinc proteins. - Kai Wang 063; Nan Lyu; Hongjuan Diao; Shujuan Jin; Tao Zeng; Yaoqi Zhou; Ruibo Wu (Bioinform., 2020)

TeroKit: A Database-Driven Web Server for Terpenome Research. - Tao Zeng; Zhihong Liu; Jingyuan Zhuang; Yitao Jiang; Wengan He; Hongjuan Diao; Nan Lv; Yongxing Jian; Danhong Liang; Yufan Qiu; Rong Zhang; Fan Zhang; et al. (J. Chem. Inf. Model., 2020)

Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases. - Jingyuan Zhuang; Fan Zhang; Jingwei Zhou; Wenbin Deng; Ruibo Wu (J. Chem. Inf. Model., 2020)

BioNavi-NP: Biosynthesis Navigator for Natural Products. - Shuangjia Zheng; Tao Zeng; Chengtao Li; Binghong Chen; Connor W. Coley; Yuedong Yang; Ruibo Wu (CoRR, 2021)

Bio-inspired chemical space exploration of terpenoids. - Tao Zeng; Bernard Andes Hess Jr.; Fan Zhang; Ruibo Wu (Briefings Bioinform., 2022)

Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit. - Nianhang Chen; Rong Zhang; Tao Zeng; Xuting Zhang; Ruibo Wu (Database J. Biol. Databases Curation, 2023)

QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis. - Fan Zhang; Tao Zeng; Ruibo Wu (J. Chem. Inf. Model., 2023)

TeroSeek: An AI-Powered Knowledge Base and Retrieval Generation Platform for Terpenoid Research. - Xu Kang 005; Siqi Jiang; Kangwei Xu; Jiahao Li; Ruibo Wu (CoRR, 2025)