Binju Wang

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 73

Top Topics

Molecular Dynamics Simulations

Electron Transfer

Machine Learning

Histone Deacetylase

Top Venues

Journal of the American Chemical Society

Angewandte Chemie (International ed. in English)

Journal of chemical information and modeling

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Bin Chen, Renjie Li, Jianqiang Feng, Beibei Zhao, Jiawei Zhang, Jinhai Yu, Yuanyuan Xu, Zhongqiu Xing, Yue Zhao, Binju Wang, Xiaoqiang Huang
Modular Access to Chiral Amines via Imine Reductase-Based Photoenzymatic Catalysis. Journal of the American Chemical Society 146 (20) (2024)
Tai-Ping Zhou, Jianqiang Feng, Yongchao Wang, Shengying Li, Binju Wang
Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS Au 4 (4) (2024)
Yuwei Hu, Jia Liu, Yujie Ke, Binju Wang, Chen Chuan Lim, Zhaogang Dong, Yi Long, Itamar Willner
Oligo-Adenine and Cyanuric Acid Supramolecular DNA-Based Hydrogels Exhibiting Acid-Resistance and Physiological pH-Responsiveness. ACS applied materials & interfaces (2024)
Yixun Jiang, Ming-Dong Yao, Jianqiang Feng, Haoran Niu, Bin Qiao, Bing-Zhi Li, Binju Wang, Wen-Hai Xiao, Min Dong, Ying-Jin Yuan
Molecular Insights into Converting Hydroxide Adenosyltransferase into Halogenase. Journal of agricultural and food chemistry (2024)
Shengheng Yan, Binju Wang, Hai Lin
Reshaping the QM Region On-the-Fly: Adaptive-Shape QM/MM Dynamic Simulations of a Hydrated Proton in Bulk Water. Journal of chemical theory and computation 20 (9) (2024)
Yuwei Hu, Jia Liu, Yujie Ke, Binju Wang, Chen Chuan Lim, Zhaogang Dong, Yi Long, Itamar Willner
Oligo-Adenine and Cyanuric Acid Supramolecular DNA-Based Hydrogels Exhibiting Acid-Resistance and Physiological pH-Responsiveness. ACS applied materials & interfaces 16 (22) (2024)
Shengheng Yan, Binju Wang, Hai Lin
Reshaping the QM Region On-the-Fly: Adaptive-Shape QM/MM Dynamic Simulations of a Hydrated Proton in Bulk Water. Journal of chemical theory and computation (2024)
Yixun Jiang, Ming-Dong Yao, Jianqiang Feng, Haoran Niu, Bin Qiao, Bing-Zhi Li, Binju Wang, Wen-Hai Xiao, Min Dong, Ying-Jin Yuan
Molecular Insights into Converting Hydroxide Adenosyltransferase into Halogenase. Journal of agricultural and food chemistry 72 (22) (2024)
Chunyan Fang, Liping Zhang, Yongchao Wang, Weiliang Xiong, Zier Yan, Wenjun Zhang, Qingbo Zhang, Binju Wang, Yiguang Zhu, Changsheng Zhang
Discovery and Biosynthesis of Cihanmycins Reveal Cytochrome P450-Catalyzed Intramolecular C-O Phenol Coupling Reactions. Journal of the American Chemical Society (2024)
Dexin Lu, Ding Luo, Yuwei Zhang, Binju Wang
A Robust Induced Fit Docking Approach with the Combination of the Hybrid All-Atom/United-Atom/Coarse-Grained Model and Simulated Annealing. Journal of chemical theory and computation 20 (14) (2024)
Qiaoyu Zhang, Qianqian Chen, Sason Shaik, Binju Wang
Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angewandte Chemie (International ed. in English) 63 (14) (2024)
Yuzhuang Fu, Jun Yu, Fangfang Fan, Binju Wang, Zexing Cao
Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations. The journal of physical chemistry. B (2024)
Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang
Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning. Journal of chemical information and modeling 64 (6) (2024)
Dexin Lu, Ding Luo, Yuwei Zhang, Binju Wang
A Robust Induced Fit Docking Approach with the Combination of the Hybrid All-Atom/United-Atom/Coarse-Grained Model and Simulated Annealing. Journal of chemical theory and computation (2024)
Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang
Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning. Journal of chemical information and modeling 64 (6) (2024)
Yuzhuang Fu, Jun Yu, Fangfang Fan, Binju Wang, Zexing Cao
Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations. The journal of physical chemistry. B 128 (23) (2024)
Qiaoyu Zhang, Qianqian Chen, Sason Shaik, Binju Wang
Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angewandte Chemie (International ed. in English) 63 (14) (2024)
Qiaoyu Zhang, Qianqian Chen, Sason Shaik, Binju Wang
Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angewandte Chemie (International ed. in English) 63 (14) (2024)
Yixun Jiang, Ming-Dong Yao, Jianqiang Feng, Haoran Niu, Bin Qiao, Bing-Zhi Li, Binju Wang, Wen-Hai Xiao, Min Dong, Ying-Jin Yuan
Molecular Insights into Converting Hydroxide Adenosyltransferase into Halogenase. Journal of agricultural and food chemistry 72 (22) (2024)
Bin Chen, Renjie Li, Jianqiang Feng, Beibei Zhao, Jiawei Zhang, Jinhai Yu, Yuanyuan Xu, Zhongqiu Xing, Yue Zhao, Binju Wang, Xiaoqiang Huang
Modular Access to Chiral Amines via Imine Reductase-Based Photoenzymatic Catalysis. Journal of the American Chemical Society (2024)
Tai-Ping Zhou, Jianqiang Feng, Yongchao Wang, Shengying Li, Binju Wang
Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS Au 4 (4) (2024)
Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang
Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning. Journal of chemical information and modeling (2024)
Qiaoyu Zhang, Qianqian Chen, Sason Shaik, Binju Wang
Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angewandte Chemie (International ed. in English) (2024)
Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang
Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning. Journal of chemical information and modeling 64 (6) (2024)
Shengheng Yan, Xinwei Ji, Wei Peng, Binju Wang
Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. The journal of physical chemistry. B 127 (19) (2023)
Wenwen Diao, James D Farrell, Binju Wang, Fangfu Ye, Zhanfeng Wang
Preorganized Internal Electric Field Promotes a Double-Displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase. The journal of physical chemistry. B (2023)
Hao Ma, Sen Yan, Xinyu Lu, Yi-Fan Bao, Jia Liu, Langxing Liao, Kun Dai, Maofeng Cao, Xiaojiao Zhao, Hao Yan, Hai-Long Wang, Xiaohui Peng, Ningyu Chen, Huishu Feng, Lilin Zhu, Guangbao Yao, Chun-Hai Fan, De-Yin Wu, Binju Wang, Xiang Wang, Bin Ren
Rapidly determining the 3D structure of proteins by surface-enhanced Raman spectroscopy. Science advances 9 (47) (2023)
Yuqing Zhang, Yanhui Chen, Qingyu Tian, Binju Wang, Guolin Cheng
Palladium-Catalyzed Multicomponent Assembly of ( Z )-Alkenylborons via Carbopalladation/Boronation/Retro-Diels-Alder Cascade Reaction. The Journal of organic chemistry (2023)
Wenhan Fang, Shishi Feng, Zhihui Jiang, WanZhen Liang, Pengfei Li, Binju Wang
Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase. JACS Au 3 (2) (2023)
Jie Chen, Jinyan Zhang, Ying Sun, Yuankai Xu, Yinan Yang, Yong-Min Lee, Wenhua Ji, Binju Wang, Wonwoo Nam, Bin Wang
Mononuclear Non-Heme Manganese-Catalyzed Enantioselective cis -Dihydroxylation of Alkenes Modeling Rieske Dioxygenases. Journal of the American Chemical Society (2023)
Wenjuan Zhu, Peng Wu, Virginia A Larson, Akhilesh Kumar, Xiao-Xi Li, Mi Sook Seo, Yong-Min Lee, Binju Wang, Nicolai Lehnert, Wonwoo Nam
Electronic Structure and Reactivity of Mononuclear Nonheme Iron-Peroxo Complexes as a Biomimetic Model of Rieske Oxygenases: Ring Size Effects of Macrocyclic Ligands. Journal of the American Chemical Society (2023)
Peijie Han, Ran Yan, Yuqing Wei, Leisu Li, Jinsong Luo, Yang Pan, Binju Wang, Jingdong Lin, Shaolong Wan, Haifeng Xiong, Yong Wang, Shuai Wang
Mechanistic Insights into Radical-Induced Selective Oxidation of Methane over Nonmetallic Boron Nitride Catalysts. Journal of the American Chemical Society (2023)
Peijie Han, Ran Yan, Yuqing Wei, Leisu Li, Jinsong Luo, Yang Pan, Binju Wang, Jingdong Lin, Shaolong Wan, Haifeng Xiong, Yong Wang, Shuai Wang
Mechanistic Insights into Radical-Induced Selective Oxidation of Methane over Nonmetallic Boron Nitride Catalysts. Journal of the American Chemical Society 145 (19) (2023)
Xitong Song, Binju Wang
O-O Bond Formation and Oxygen Release in Photosystem II Are Enhanced by Spin-Exchange and Synergetic Coordination Interactions. Journal of chemical theory and computation (2023)
Wenhan Fang, Shishi Feng, Zhihui Jiang, WanZhen Liang, Pengfei Li, Binju Wang
Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase. JACS Au 3 (2) (2023)
Wenjuan Zhu, Peng Wu, Virginia A Larson, Akhilesh Kumar, Xiao-Xi Li, Mi Sook Seo, Yong-Min Lee, Binju Wang, Nicolai Lehnert, Wonwoo Nam
Electronic Structure and Reactivity of Mononuclear Nonheme Iron-Peroxo Complexes as a Biomimetic Model of Rieske Oxygenases: Ring Size Effects of Macrocyclic Ligands. Journal of the American Chemical Society 146 (1) (2023)
Zhanfeng Wang, Wenwen Diao, Peng Wu, Junfeng Li, Yuzhuang Fu, Zhiyong Guo, Zexing Cao, Sason S Shaik, Binju Wang
How the Conformational Movement of the Substrate Drives the Regioselective C-N Bond Formation in P450 TleB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. Journal of the American Chemical Society (2023)
Wenjuan Zhu, Peng Wu, Virginia A Larson, Akhilesh Kumar, Xiao-Xi Li, Mi Sook Seo, Yong-Min Lee, Binju Wang, Nicolai Lehnert, Wonwoo Nam
Electronic Structure and Reactivity of Mononuclear Nonheme Iron-Peroxo Complexes as a Biomimetic Model of Rieske Oxygenases: Ring Size Effects of Macrocyclic Ligands. Journal of the American Chemical Society 146 (1) (2023)
Zhiyong Guo, Lei Wang, Deming Rao, Weiqiong Liu, Miaomiao Xue, Qisheng Fu, Mengwei Lu, Lingqia Su, Sheng Chen, Binju Wang, Jing Wu
Conformational Switch of the 250s Loop Enables the Efficient Transglycosylation in GH Family 77. Journal of chemical information and modeling (2023)
Lina Dong, Shuai Shi, Xiaoyang Qu, Ding Luo, Binju Wang
Ligand binding affinity prediction with fusion of graph neural networks and 3D structure-based complex graph. Physical chemistry chemical physics : PCCP (2023)
Shengheng Yan, Xinwei Ji, Wei Peng, Binju Wang
Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. The journal of physical chemistry. B 127 (19) (2023)
Shengheng Yan, Xinwei Ji, Wei Peng, Binju Wang
Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. The journal of physical chemistry. B (2023)
Xiaoyang Qu, Lina Dong, Ding Luo, Yu-Bing Si, Binju Wang
Water Network-Augmented Two-State Model for Protein-Ligand Binding Affinity Prediction. Journal of chemical information and modeling (2023)
Kai Liu, Jinyan Zhang, Guangtao Zhang, Liping Zhang, Zhen Meng, Liang Ma, Wenjun Zhang, Weiliang Xiong, Yiguang Zhu, Binju Wang, Changsheng Zhang
Deciphering Deoxynybomycin Biosynthesis Reveals Fe(II)/α-Ketoglutarate-Dependent Dioxygenase-Catalyzed Oxazoline Ring Formation and Decomposition. Journal of the American Chemical Society (2023)
Wenjuan Zhu, Peng Wu, Virginia A Larson, Akhilesh Kumar, Xiao-Xi Li, Mi Sook Seo, Yong-Min Lee, Binju Wang, Nicolai Lehnert, Wonwoo Nam
Electronic Structure and Reactivity of Mononuclear Nonheme Iron-Peroxo Complexes as a Biomimetic Model of Rieske Oxygenases: Ring Size Effects of Macrocyclic Ligands. Journal of the American Chemical Society 146 (1) (2023)
Shengheng Yan, Binju Wang, Hai Lin
Tracking the Delocalized Proton in Concerted Proton Transfer in Bulk Water. Journal of chemical theory and computation (2023)
Linlin Wang, Zhihui Jiang, Jiahe Zhang, Kuan Chen, Meng Zhang, Zi-Long Wang, Binju Wang, Min Ye, Xue Qiao
Characterization and structure-based protein engineering of a regiospecific saponin acetyltransferase from Astragalus membranaceus. Nature communications 14 (1) (2023)
Yuzhuang Fu, Binju Wang, Zexing Cao
Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O-O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations. Inorganic chemistry (2022)
Jianhua Wei, Xuan Zhang, Yucong Zhou, Xingnuo Cheng, Zhi Lin, Man-Cheng Tang, Jianting Zheng, Binju Wang, Qianjin Kang, Linquan Bai
Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies. Nature communications 13 (1) (2022)
Xiaoyang Qu, Lina Dong, Jinyan Zhang, Yu-Bing Si, Binju Wang
Systematic Improvement of the Performance of Machine Learning Scoring Functions by Incorporating Features of Protein-Bound Water Molecules. Journal of chemical information and modeling 62 (18) (2022)
Binju Wang, Xuan Zhang, Wenhan Fang, Carme Rovira, Sason S Shaik
How Do Metalloproteins Tame the Fenton Reaction and Utilize •OH Radicals in Constructive Manners? Accounts of chemical research 55 (16) (2022)
Lina Dong, Xiaoyang Qu, Binju Wang
XLPFE: A Simple and Effective Machine Learning Scoring Function for Protein-Ligand Scoring and Ranking. ACS omega 7 (25) (2022)
Tzu-Yu Chen, Ziyang Zheng, Xuan Zhang, Jinfeng Chen, Lide Cha, Yijie Tang, Yisong Guo, Jiahai Zhou, Binju Wang, Hung-Wen Liu, Wei-Chen Chang
Deciphering the Reaction Pathway of Mononuclear Iron Enzyme-Catalyzed N≡C Triple Bond Formation in Isocyanide Lipopeptide and Polyketide Biosynthesis. ACS catalysis 12 (4) (2022)
Peng Wu, Shengheng Yan, Wenhan Fang, Binju Wang
Molecular Mechanism of the Mononuclear Copper Complex-Catalyzed Water Oxidation from Cluster-Continuum Model Calculations. ChemSusChem 15 (7) (2022)
Peng Wu, Yang Gu, Langxing Liao, Yanfei Wu, Jiaoyu Jin, Zhanfeng Wang, Jiahai Zhou, Sason Shaik, Binju Wang
Coordination Switch Drives Selective C-S Bond Formation by the Non-Heme Sulfoxide Synthases. Angewandte Chemie (International ed. in English) 61 (50) (2022)
Yuzhuang Fu, Yuwei Zhang, Fangfang Fan, Binju Wang, Zexing Cao
Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulations. Physical chemistry chemical physics : PCCP 24 (2) (2022)
Xiaoyang Qu, Lina Dong, Yu-Bing Si, Yuan Zhao, Qiantao Wang, Peifeng Su, Binju Wang
Reliable Prediction of the Protein-Ligand Binding Affinity Using a Charge Penetration Corrected AMOEBA Force Field: A Case Study of Drug Resistance Mutations in Abl Kinase. Journal of chemical theory and computation 18 (3) (2022)
Zhiyong Guo, Lei Wang, Lingqia Su, Sheng Chen, Wei Xia, Isabelle André, Carme Rovira, Binju Wang, Jing Wu
A Single Hydrogen Bond Controls the Selectivity of Transglycosylation vs Hydrolysis in Family 13 Glycoside Hydrolases. The journal of physical chemistry letters 13 (24) (2022)
Yu-Hsuan Lee, Xueli Hou, Ridao Chen, Jianqiang Feng, Xiao Liu, Mark W Ruszczycky, Jin-Ming Gao, Binju Wang, Jiahai Zhou, Hung-Wen Liu
Radical S -Adenosyl Methionine Enzyme BlsE Catalyzes a Radical-Mediated 1,2-Diol Dehydration during the Biosynthesis of Blasticidin S. Journal of the American Chemical Society 144 (10) (2022)
Binju Wang, Peng Wu, Sason S Shaik
Critical Roles of Exchange and Superexchange Interactions in Dictating Electron Transfer and Reactivity in Metalloenzymes. The journal of physical chemistry letters 13 (13) (2022)
Wei Peng, Shengheng Yan, Xuan Zhang, Langxing Liao, Jinyan Zhang, Sason S Shaik, Binju Wang
How Do Preorganized Electric Fields Function in Catalytic Cycles? The Case of the Enzyme Tyrosine Hydroxylase. Journal of the American Chemical Society 144 (44) (2022)
Ronny L Cheng, Chun Wu, Zexing Cao, Binju Wang
QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase. Physical chemistry chemical physics : PCCP 22 (36) (2021)
Zhanfeng Wang, Sason S Shaik, Binju Wang
Conformational Motion of Ferredoxin Enables Efficient Electron Transfer to Heme in the Full-Length P450TT. Journal of the American Chemical Society 143 (2) (2021)
Conger Wang, Peng Wu, Zhanfeng Wang, Binju Wang
The molecular mechanism of P450-catalyzed amination of the pyrrolidine derivative of lidocaine: insights from multiscale simulations. RSC advances 11 (44) (2021)
Guiyun Zhao, Wei Peng, Kaihui Song, Jingkun Shi, Xingyu Lu, Binju Wang, Yi-Ling Du
Molecular basis of enzymatic nitrogen-nitrogen formation by a family of zinc-binding cupin enzymes. Nature communications 12 (1) (2021)
Lina Dong, Xiaoyang Qu, Yuan Zhao, Binju Wang
Prediction of Binding Free Energy of Protein-Ligand Complexes with a Hybrid Molecular Mechanics/Generalized Born Surface Area and Machine Learning Method. ACS omega 6 (48) (2021)
Jianqiang Feng, Sason Shaik, Binju Wang
Spin-Regulated Electron Transfer and Exchange-Enhanced Reactivity in Fe4 S4 -Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angewandte Chemie (International ed. in English) 60 (37) (2021)
Jian-Bo Wang, Qun Huang, Wei Peng, Peng Wu, Da Yu, Yongning Wu, Binju Wang, Manfred T Reetz
P450-BM3-Catalyzed Sulfoxidation versus Hydroxylation: A Common or Two Different Catalytically Active Species? Journal of the American Chemical Society 142 (4) (2020)
Zhanfeng Wang, Shishi Feng, Carme Rovira, Binju Wang
How Oxygen Binding Enhances Long-Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase. Angewandte Chemie (International ed. in English) 60 (5) (2020)
Hao Su, Binju Wang, Sason S Shaik
Quantum-Mechanical/Molecular-Mechanical Studies of CYP11A1-Catalyzed Biosynthesis of Pregnenolone from Cholesterol Reveal a C-C Bond Cleavage Reaction That Occurs by a Compound I-Mediated Electron Transfer. Journal of the American Chemical Society 141 (51) (2019)
Binju Wang, Zexing Cao, Carme Rovira, Jinshuai Song, Sason S Shaik
Fenton-Derived OH Radicals Enable the MPnS Enzyme to Convert 2-Hydroxyethylphosphonate to Methylphosphonate: Insights from Ab Initio QM/MM MD Simulations. Journal of the American Chemical Society 141 (23) (2019)
Peng Wu, Fangfang Fan, Jinshuai Song, Wei Peng, Jia Liu, Chun-Sen Li, Zexing Cao, Binju Wang
Theory Demonstrated a "Coupled" Mechanism for O2 Activation and Substrate Hydroxylation by Binuclear Copper Monooxygenases. Journal of the American Chemical Society 141 (50) (2019)
Binju Wang, Sason S Shaik
The Nickel-Pincer Complex in Lactate Racemase Is an Electron Relay and Sink that acts through Proton-Coupled Electron Transfer. Angewandte Chemie (International ed. in English) 56 (34) (2017)