Ruibo Wu

发表

Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase

Wei Wu, Ruibo Wu, Xin Zhang, 2009, J. Comput. Chem..

A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions.

Ruibo Wu, Z. Cao, Yingkai Zhang, 2010, Journal of the American Chemical Society.

Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel.

Ruibo Wu, Z. Cao, Yingkai Zhang, 2011, Journal of the American Chemical Society.

Computational Design of a Time-Dependent Histone Deacetylase 2 Selective Inhibitor

Ruibo Wu, Yingkai Zhang, Shenglong Wang, 2014, ACS chemical biology.

Conformational dynamics and allosteric effect modulated by the unique zinc-binding motif in class IIa HDACs.

Ruibo Wu, Huawei Liu, Fan Zhang, 2019, Physical chemistry chemical physics : PCCP.

Deciphering the mechanisms of selective inhibition for the tandem BD1/BD2 in the BET-bromodomain family.

Ruibo Wu, Fan Zhang, Kai Wang, 2017, Physical chemistry chemical physics : PCCP.

Protonation-Dependent Diphosphate Cleavage in FPP Cyclases and Synthases

Ruibo Wu, Jingwei Zhou, N. Chen, 2016 .

Catalytic promiscuity of the non-native FPP substrate in the TEAS enzyme: non-negligible flexibility of the carbocation intermediate.

Ruibo Wu, Fan Zhang, Xiaowen Tang, 2018, Physical chemistry chemical physics : PCCP.

Intrinsic Dynamics of the Binding Rail and Its Allosteric Effect in the Class I Histone Deacetylases

Ruibo Wu, Jingwei Zhou, Kai Wang, 2017, J. Chem. Inf. Model..

Inhibition mechanism of SAHA in HDAC: a revisit.

Ruibo Wu, Jingwei Zhou, Hai-bin Luo, 2015, Physical chemistry chemical physics : PCCP.

Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase.

Ruibo Wu, Z. Cao, N. Chen, 2015, Journal of chemical theory and computation.

A salt bridge turns off the foot-pocket in class-II HDACs.

Ruibo Wu, Jingwei Zhou, Hai-bin Luo, 2016, Physical chemistry chemical physics : PCCP.

Mechanistic studies for tri-targeted inhibition of enzymes involved in cholesterol biosynthesis by green tea polyphenols.

Ruibo Wu, Ding Li, Jun Xu, 2014, Organic & biomolecular chemistry.

A conserved mechanism affecting hydride shifting and deprotonation in the synthesis of hopane triterpenes as compositions of wax in oat

Ruibo Wu, Fan Zhang, Miaomiao Liang, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Structure-based drug design: Synthesis and biological evaluation of quinazolin-4-amine derivatives as selective Aurora A kinase inhibitors.

Quentin Liu, Ruibo Wu, Min Yan, 2018, European journal of medicinal chemistry.

Asymmetric Counter-Anion-Directed Aminomethylation: Synthesis of Chiral β-Amino Acids via Trapping of an Enol Intermediate.

Ruibo Wu, Yongheng Wang, Wenhao Hu, 2019, Journal of the American Chemical Society.

Structure-Based Design of 5-Methylpyrimidopyridone Derivatives as New Wild-Type Sparing Inhibitors of Epidermal Growth Factor Receptor Triple Mutant (EGFRL858R/T790M/C797S).

Wei Xu, Ruibo Wu, Jian Ding, 2019, Journal of medicinal chemistry.

Borane-Catalyzed Chemoselectivity-Controllable N-Alkylation and ortho C-Alkylation of Unprotected Arylamines Using Benzylic Alcohols

A. Chan, Ruibo Wu, Xiaowen Tang, 2019, ACS Catalysis.

Exploring the interstitial atom in the FeMo cofactor of nitrogenase: insights from QM and QM/MM calculations.

Ruibo Wu, Z. Cao, Zhaohui Zhou, 2008, The journal of physical chemistry. B.

Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP

Connor W. Coley, Yuedong Yang, Chengtao Li, 2022, Nature Communications.

Rationally engineering santalene synthase to readjust the component ratio of sandalwood oil

Jiachen Zi, Ruibo Wu, Fan Zhang, 2022, Nature Communications.

Structural studies reveal flexible roof of active site responsible for ω-transaminase CrmG overcoming by-product inhibition

Ruibo Wu, Weiming Zhu, Yiguang Zhu, 2020, Communications Biology.

Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase-5.

Ruibo Wu, Hai-bin Luo, Zhe Li, 2014, Journal of chemical theory and computation.

Interaction mechanism between zein and β-lactoglobulin: Insights from multi-spectroscopy and molecular dynamics simulation methods

Ruibo Wu, Z. Cao, Hujun Xie, 2022, Food Hydrocolloids.

An Unexpected Oxidosqualene Cyclase Active Site Architecture in the Iris tectorum Multifunctional α-Amyrin Synthase.

Ruibo Wu, I. Molnár, Fan Zhang, 2020, ACS catalysis.

Robust RNA structure refinement by a nucleobase-centric sampling algorithm coupled with a backbone rotameric and quantum-mechanical-energy-scaled base-base knowledge-based potential.

Yaoqi Zhou, J. Zhan, Ruibo Wu, 2021 .

Loop motion and base release in purine-specific nucleoside hydrolase: a molecular dynamics study.

Ruibo Wu, Z. Cao, Jun Xu, 2013, Biochimica et biophysica acta.

QM/MM molecular dynamics study of purine-specific nucleoside hydrolase.

Ruibo Wu, Z. Cao, Yingkai Zhang, 2012, The journal of physical chemistry. B.

Discovery and optimization of α-mangostin derivatives as novel PDE4 inhibitors for the treatment of vascular dementia.

Steven H. Liang, Ruibo Wu, Hai-bin Luo, 2020, Journal of medicinal chemistry.

Computer-assisted designed "selenoxy-chinolin": a new catalytic mechanism of the GPx-like cycle and inhibition of metal-free and metal-associated Aβ aggregation.

Ruibo Wu, Zhihong Liu, Xingshu Li, 2015, Dalton transactions.

AromTool: predicting aromatic stacking energy using an atomic neural network model.

Ruibo Wu, Kai Wang, Hongjuan Diao, 2021, Physical chemistry chemical physics : PCCP.

Explore the interaction mechanism between zein and EGCG using multi-spectroscopy and molecular dynamics simulation methods

Ruibo Wu, Z. Cao, Hujun Xie, 2021 .

Combined quantum mechanics/molecular mechanics study on the reversible isomerization of glucose and fructose catalyzed by Pyrococcus furiosus phosphoglucose isomerase.

Y. Mo, Ruibo Wu, Z. Cao, 2008, Journal of the American Chemical Society.

Chemotaxonomic Investigation of Plant Terpenoids with an Established Database (TeroMOL).

Ruibo Wu, Tao Zeng, Fan Zhang, 2022, The New phytologist.

Recognition of PDL1/L2 by different induced-fit mechanisms of PD1: a comparative study of molecular dynamics simulations.

Yi Zhao, Ruibo Wu, Yubing Si, 2019, Physical chemistry chemical physics : PCCP.

Development of a Smart Fluorescent Sensor That Specifically Recognizes the c-MYC G-Quadruplex.

Ruibo Wu, Shuo-Bin Chen, Zhishu Huang, 2019, Analytical chemistry.

Catalytic role of carbonyl oxygens and water in selinadiene synthase

Jeroen S. Dickschat, X. Chen, Ruibo Wu, 2022, Nature Catalysis.

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, Ruibo Wu, 2008, J. Comput. Chem..

TeroKit: A Database-Driven Web Server for Terpenome Research

Ruibo Wu, Xiaowen Tang, Fan Zhang, 2020, J. Chem. Inf. Model..

Pine pollen inhibits cell apoptosis-related protein expression in the cerebral cortex of mice with arsenic poisoning

Ruibo Wu, Yanhong Luo, Yaodong Wei, 2012, Neural regeneration research.

Binding Kinetics versus Affinities in BRD4 Inhibition

Ruibo Wu, Jingwei Zhou, Zhihong Liu, 2015, J. Chem. Inf. Model..

Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

Yaoqi Zhou, J. Zhan, Ruibo Wu, 2021, Nature Communications.

Enzymatic Plasticity Inspired by the Diterpene Cyclase CotB2.

Ruibo Wu, Fan Zhang, Xiaowen Tang, 2020, ACS chemical biology.

Structure-Function Analysis of the Conserved Tyrosine and Diverse π-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study

Ruibo Wu, Jingwei Zhou, Zhihong Liu, 2014, J. Chem. Inf. Model..

Molecular Dynamics Simulations of the Detoxification of Paraoxon Catalyzed by Phosphotriesterase ( PTE )

Lingchun Song, Wei Wu, Y. Mo, 2011 .

Covalent Inhibition Mechanism of Antidiabetic Drugs—Vildagliptin vs Saxagliptin

Ruibo Wu, Fan Zhang, Hongjuan Diao, 2019, ACS Catalysis.

Structure-based discovery of potent and selective small-molecule inhibitors targeting signal transducer and activator of transcription 3 (STAT3).

Ruibo Wu, Lin Deng, Peiqing Liu, 2021, European journal of medicinal chemistry.

Multiscale Simulations on the Catalytic Plasticity of CYP76AH1

Ruibo Wu, Hongjuan Diao, Ying Zheng, 2021, Frontiers in Chemistry.

Bio-inspired chemical space exploration of terpenoids

Ruibo Wu, Tao Zeng, Fan Zhang, 2022, Briefings Bioinform..

Biosynthetic Mechanism of Lanosterol: Cyclization.

Ruibo Wu, Nanhao Chen, Shenglong Wang, 2015, Angewandte Chemie.

Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An ab Initio QM/MM MD Study.

Ruibo Wu, Nanhao Chen, Jun Xu, 2014, Journal of chemical theory and computation.

Biosynthetic Mechanism of Lanosterol: A Completed Story

Ruibo Wu, N. Chen, Fan Zhang, 2020, ACS Catalysis.

Enzyme Promiscuity versus Fidelity in Two Sesquiterpene Cyclases (TEAS versus ATAS)

Jiachen Zi, Ruibo Wu, Hai-bin Luo, 2020 .

Protonation-Triggered Carbon-Chain Elongation in Geranyl Pyrophosphate Synthase (GPPS)

Ruibo Wu, Yirong Mo, Ming Kuang, 2015 .

Mechanism of Assembling Isoprenoid Building Blocks 1. Elucidation of the Structural Motifs for Substrate Binding in Geranyl Pyrophosphate Synthase.

Ruibo Wu, Jun Xu, Ruibo Wu, 2014, Journal of chemical theory and computation.

Structural studies reveal flexible roof of active site responsible for ω-transaminase CrmG overcoming by-product inhibition

Ruibo Wu, Weiming Zhu, Yiguang Zhu, 2020, Communications Biology.

Proton-Shuttle-Assisted Heterolytic Carbon–Carbon Bond Cleavage and Formation

Ruibo Wu, Zexing Cao, Yirong Mo, 2015 .

GM-DockZn: a geometry matching-based docking algorithm for zinc proteins

Yaoqi Zhou, Kai Wang, Tao Zeng, 2020, Bioinform..

Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS

Fan Zhang, Ruibo Wu, Nanhao Chen, 2016, J. Chem. Inf. Model..

Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study

Ruibo Wu, Yingkai Zhang, Wenjing Gong, 2015, J. Comput. Chem..

Unnatural activities and mechanistic insights of cytochrome P450 PikC gained from site-specific mutagenesis by non-canonical amino acids

Ruibo Wu, Xiang Gao, Guobang Li, 2023, Nature Communications.

Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity

Ruibo Wu, Jingwei Zhou, Hujun Xie, 2017 .

pH-dependent interaction mechanisms between β-lactoglobulin and EGCG: Insights from multi-spectroscopy and molecular dynamics simulation methods

Ruibo Wu, Z. Cao, Hujun Xie, 2022, Food Hydrocolloids.

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study.

Ruibo Wu, Zexing Cao, Yingkai Zhang, 2010, Journal of chemical theory and computation.

Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase

Ruibo Wu, L. Meng, Yuanyuan Jiang, 2023, Nature Communications.

Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases

Ruibo Wu, Jingwei Zhou, Fan Zhang, 2020, J. Chem. Inf. Model..

A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase.

Ruibo Wu, Nanhao Chen, Zexing Cao, 2014, Physical chemistry chemical physics : PCCP.

Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing

Ruibo Wu, Yu Wang, Jun Xu, 2013, J. Chem. Inf. Model..

Structure-based drug design: Synthesis and biological evaluation of quinazolin-4-amine derivatives as selective Aurora A kinase inhibitors.

Quentin Liu, Ruibo Wu, Min Yan, 2018, European journal of medicinal chemistry.

Exploring Chemical and Biological Space of Terpenoids

Ruibo Wu, Xiaowen Tang, Zhihong Liu, 2019, J. Chem. Inf. Model..

Structural Insights into Three Sesquiterpene Synthases for the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion by Structure-Based Mutagenesis.

Jeroen S. Dickschat, Ruibo Wu, M. Ma, 2023, Journal of the American Chemical Society.

QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis.

Ruibo Wu, Tao Zeng, Fan Zhang, 2023, Journal of chemical information and modeling.

Discovering a uniform functional trade-off of the CBC-type 2,3-oxidosqualene cyclases and deciphering its chemical logic

Ruibo Wu, Fan Zhang, A. Ji, 2023, Science advances.

Biosynthesis of Spinosyn A: A [4 + 2] or [6 + 4] Cycloaddition?

Ruibo Wu, N. Chen, Fan Zhang, 2018 .

Zinc chelation with hydroxamate in histone deacetylases modulated by water access to the linker binding channel.

Ruibo Wu, Z. Cao, Yingkai Zhang, 2011, Journal of the American Chemical Society.

Mechanistic studies for tri-targeted inhibition of enzymes involved in cholesterol biosynthesis by green tea polyphenols.

Ruibo Wu, Ding Li, Jun Xu, 2014, Organic & biomolecular chemistry.

A salt bridge turns off the foot-pocket in class-II HDACs.

Ruibo Wu, Jingwei Zhou, Hai-bin Luo, 2016, Physical Chemistry, Chemical Physics - PCCP.

A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins.

Ruibo Wu, Zexing Cao, Yingkai Zhang, 2011, Journal of chemical theory and computation.

NIMO: A Natural Product-Inspired Molecular Generative Model Based on Conditional Transformer

Ruibo Wu, Xiaojuan Shen, Tao Zeng, 2024, Molecules.

Developing BioNavi for Hybrid Retrosynthesis Planning

Ruibo Wu, Tao Zeng, Zhehao Jin, 2024, JACS Au.