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Your search keyword '"Huang, Niu"' showing total 362 results
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362 results on '"Huang, Niu"'

1. The need to implement FAIR principles in biomolecular simulations

Author

Amaro, Rommie, Åqvist, Johan, Bahar, Ivet, Battistini, Federica, Bellaiche, Adam, Beltran, Daniel, Biggin, Philip C., Bonomi, Massimiliano, Bowman, Gregory R., Bryce, Richard, Bussi, Giovanni, Carloni, Paolo, Case, David, Cavalli, Andrea, Chang, Chie-En A., Cheatham III, Thomas E., Cheung, Margaret S., Chipot, Cris, Chong, Lillian T., Choudhary, Preeti, Cisneros, Gerardo Andres, Clementi, Cecilia, Collepardo-Guevara, Rosana, Coveney, Peter, Covino, Roberto, Crawford, T. Daniel, Peraro, Matteo Dal, de Groot, Bert, Delemotte, Lucie, De Vivo, Marco, Essex, Jonathan, Fraternali, Franca, Gao, Jiali, Gelpí, Josep Lluís, Gervasio, Francesco Luigi, Gonzalez-Nilo, Fernando Danilo, Grubmüller, Helmut, Guenza, Marina, Guzman, Horacio V., Harris, Sarah, Head-Gordon, Teresa, Hernandez, Rigoberto, Hospital, Adam, Huang, Niu, Huang, Xuhui, Hummer, Gerhard, Iglesias-Fernández, Javier, Jensen, Jan H., Jha, Shantenu, Jiao, Wanting, Jorgensen, William L., Kamerlin, Shina Caroline Lynn, Khalid, Syma, Laughton, Charles, Levitt, Michael, Limongelli, Vittorio, Lindahl, Erik, Lindorff-Larsen, Kresten, Loverde, Sharon, Lundborg, Magnus, Luo, Yun Lyna, Luque, Francisco Javier, Lynch, Charlotte I., MacKerell, Alexander, Magistrato, Alessandra, Marrink, Siewert J., Martin, Hugh, McCammon, J. Andrew, Merz, Kenneth, Moliner, Vicent, Mulholland, Adrian, Murad, Sohail, Naganathan, Athi N., Nangia, Shikha, Noe, Frank, Noy, Agnes, Oláh, Julianna, O'Mara, Megan, Ondrechen, Mary Jo, Onuchic, José N., Onufriev, Alexey, Osuna, Silvia, Panchenko, Anna R., Pantano, Sergio, Parish, Carol, Parrinello, Michele, Perez, Alberto, Perez-Acle, Tomas, Perilla, Juan R., Pettitt, B. Montgomery, Pietropalo, Adriana, Piquemal, Jean-Philip, Poma, Adolfo, Praprotnik, Matej, Ramos, Maria J., Ren, Pengyu, Reuter, Nathalie, Roitberg, Adrian, Rosta, Edina, Rovira, Carme, Roux, Benoit, Röthlisberger, Ursula, Sanbonmatsu, Karissa Y., Schlick, Tamar, Shaytan, Alexey K., Simmerling, Carlos, Smith, Jeremy C., Sugita, Yuji, Świderek, Katarzyna, Taiji, Makoto, Tao, Peng, Tikhonova, Irina G., Tirado-Rives, Julian, Tunón, Inaki, Van Der Kamp, Marc W., Van der Spoel, David, Velankar, Sameer, Voth, Gregory A., Wade, Rebecca, Warshel, Ariel, Welborn, Valerie Vaissier, Wetmore, Stacey, Wong, Chung F., Yang, Lee-Wei, Zacharias, Martin, and Orozco, Modesto

Subjects
Quantitative Biology - Biomolecules
Abstract

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/)

Published
2024

16. Structure-Based Identification of Kelch-like ECH-Associated Protein 1 as a Pharmacological Target of Electrophile-Containing Catechol-O-Methyltransferase Inhibitors

Author

Wang, Ping, primary, Li, Yang, additional, Yang, Jinyi, additional, Li, Ziwen, additional, Ren, Xintong, additional, Meng, Qingshi, additional, Li, Pengfei, additional, Qin, Luzhe, additional, Li, Wei, additional, Xie, Yuting, additional, Hou, Nannan, additional, and Huang, Niu, additional

Published
2024
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19. Amorphous MnO2 Lamellae Encapsulated Covalent Triazine Polymer‐Derived Multi‐Heteroatoms‐Doped Carbon for ORR/OER Bifunctional Electrocatalysis

Author

Huo, Liping, primary, Lv, Minghui, additional, Li, Mingjin, additional, Ni, Xuepeng, additional, Guan, Jingyu, additional, Liu, Jian, additional, Mei, Shuxing, additional, Yang, Yuqi, additional, Zhu, Miaomiao, additional, Feng, Qichun, additional, Geng, Peng, additional, Hou, Jianhua, additional, Huang, Niu, additional, Liu, Wei, additional, Kong, Xin Ying, additional, Zheng, Yong, additional, and Ye, Liqun, additional

Published
2024
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25. Structure of protein O-mannose kinase reveals a unique active site architecture.

Author

Zhu, Qinyu, Venzke, David, Walimbe, Ameya S, Anderson, Mary E, Fu, Qiuyu, Kinch, Lisa N, Wang, Wei, Chen, Xing, Grishin, Nick V, Huang, Niu, Yu, Liping, Dixon, Jack E, Campbell, Kevin P, and Xiao, Junyu

Subjects
Animals, Zebrafish, Humans, Baculoviridae, Aluminum Compounds, Fluorides, Magnesium, Protein Kinases, Mannose, Trisaccharides, Dystroglycans, Fish Proteins, Recombinant Proteins, Adenosine Diphosphate, Crystallography, X-Ray, Cloning, Molecular, Sequence Alignment, Gene Expression, Amino Acid Sequence, Catalytic Domain, Protein Binding, Sequence Homology, Amino Acid, Substrate Specificity, Phosphorylation, Mutation, Models, Molecular, Protein Interaction Domains and Motifs, Sf9 Cells, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, biochemistry, biophysics, dystroglycan biosynthesis, muscular dystrophy, none, secretory pathway kinase, structural biology, Crystallography, X-Ray, Cloning, Molecular, Sequence Homology, Amino Acid, Models, Protein Conformation, alpha-Helical, beta-Strand, 1.1 Normal biological development and functioning, Generic Health Relevance, Biochemistry and Cell Biology
Abstract

The 'pseudokinase' SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on α-dystroglycan. However, the catalytic mechanism underlying this activity remains elusive. Here we present the crystal structure of Danio rerio POMK in complex with Mg2+ ions, ADP, aluminum fluoride, and the GalNAc-β3-GlcNAc-β4-Man trisaccharide substrate, thereby providing a snapshot of the catalytic transition state of this unusual kinase. The active site of POMK is established by residues located in non-canonical positions and is stabilized by a disulfide bridge. GalNAc-β3-GlcNAc-β4-Man is recognized by a surface groove, and the GalNAc-β3-GlcNAc moiety mediates the majority of interactions with POMK. Expression of various POMK mutants in POMK knockout cells further validated the functional requirements of critical residues. Our results provide important insights into the ability of POMK to function specifically as a glycan kinase, and highlight the structural diversity of the human kinome.

Published
2016

27. Precisely Engineering Asymmetric Atomic CoN4 by Electron Donating and Extracting for Oxygen Reduction Reaction.

Author

Lv, Minghui, Cui, Cheng‐Xing, Huang, Niu, Wu, Mingzhu, Wang, Qiao, Gao, Tao, Zheng, Yong, Li, Hui, Liu, Wei, Huang, Yingping, Ma, Tianyi, and Ye, Liqun

Subjects
CATALYTIC activity, ELECTRON density, COBALT catalysts, ELECTRONS, ELECTROCATALYSTS, CATALYSTS
Abstract

The development of nonpyrolytic catalysts featuring precisely defined active sites represents an effective strategy for investigating the fundamental relationship between the catalytic activity of oxygen reduction reaction (ORR) catalysts and their local coordination environments. In this study, we have synthesized a series of model electrocatalysts with well‐defined CoN4 centers and nonplanar symmetric coordination structures. These catalysts were prepared by a sequential process involving the chelation of cobalt salts and 1,10‐phenanthroline‐based ligands with various substituent groups (phen(X), where X=OH, CH3, H, Br, Cl) onto covalent triazine frameworks (CTFs). By modulating the electron‐donating or electron‐withdrawing properties of the substituent groups on the phen‐based ligands, the electron density surrounding the CoN4 centers was effectively controlled. Our results demonstrated a direct correlation between the catalytic activity of the CoN4 centers and the electron‐donating ability of the substituent group on the phenanthroline ligands. Notably, the catalyst denoted as BCTF−Co‐phen(OH), featuring the electron‐donating OH group, exhibited the highest ORR catalytic activity. This custom‐crafted catalyst achieved a remarkable half‐wave potential of up to 0.80 V vs. RHE and an impressive turnover frequency (TOF) value of 47.4×10−3 Hz at 0.80 V vs. RHE in an alkaline environment. [ABSTRACT FROM AUTHOR]

Published
2024
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41. Affine combination‐based over‐sampling for imbalanced regression.

Author

Li, Zhen‐Zhen, Huang, Niu, Yi, Lun‐Zhao, and Fu, Guang‐Hui

Subjects
*PREDICTION models, *DATA distribution, *DATA mining
Abstract

Imbalanced domain prediction analysis is currently one of the hot research topics. Many real‐world data mining analyses involve using imbalanced data to obtain predictive models. In the context of imbalance, research on classification problems has been extensive, but research on regression problems is negligible. Rare values rarely occur in imbalanced regression problems, but the focus is on accurately predicting the continuous target variables of rare instances. One of the challenges in imbalanced regression is finding a suitable strategy to rebalance the original dataset in order to improve the predictive performance of the model in rare instances. In this study, two algorithms are proposed: sigma nearest over‐sampling based on convex combination for regression (SNOCCR) and affine combination‐based over‐sampling (ACOS). ACOS rebalances the original dataset by generating new instances through the affine combinations of the original examples. The region where the new instances are generated can be adjusted based on the distribution of the data, ensuring that the generated cases better mimic the distribution of the original examples. The comparison among ACOS, SNOCCR, and other preprocessing methods was conducted on 15 datasets to validate the predictive performance of models trained on rebalanced datasets for rare instances. The experimental results indicate that ACOS outperforms other existing methods. In this study, two over‐sampling algorithms are proposed: sigma nearest over‐sampling based on convex combination for regression (SNOCCR) and affine combination‐based over‐sampling (ACOS) in order to improve the predictive performance of the model in imbalanced regression. The experimental results indicate that ACOS outperforms other existing methods. [ABSTRACT FROM AUTHOR]

Published
2024
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