The need to implement FAIR principles in biomolecular simulations

Authors: 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, Orozco, Modesto

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2407.16584

Mechanistic insights into the orthogonal functionality of an AHL-mediated quorum-sensing circuit in Yersinia pseudotuberculosis

Authors: Luo, Boyu, Wu, Shanshan, Liu, Wei, Zhang, Dongdong, Liu, Ruicun, Liu, Tuoyu, Sun, Zhi, Wei, Ziqun, Liu, Mingyu, Shi, Zhiyuan, Huang, Niu, Teng, Yue

Source: In Synthetic and Systems Biotechnology 2025 10(1):174-184

Selective degradation of multimeric proteins by TRIM21-based molecular glue and PROTAC degraders

Authors: Lu, Panrui, Cheng, Yalong, Xue, Lei, Ren, Xintong, Xu, Xilong, Chen, Chenglong, Cao, Longzhi, Li, Jiaojiao, Wu, Qingcui, Sun, Shan, Hou, Junjie, Jia, Wei, Wang, Wei, Ma, Yan, Jiang, Zhaodi, Li, Chao, Qi, Xiangbing, Huang, Niu, Han, Ting

Source: In Cell 12 December 2024 187(25):7126-7142

Exploring structure-based drug discovery of GPCRs beyond the orthosteric binding site

Authors: Chen, Zhao, Ren, Xintong, Zhou, Yu, Huang, Niu

Source: In hLife May 2024 2(5):211-226

Simultaneously Regulating charge separation and proton supply-demand in polyphenol amine for hydrogen peroxide photosynthesis

Authors: Xu, Run, Liu, Wei, Deng, Yihan, Gao, Rong, Huang, Niu, Zheng, Yong, Huang, Yingping, Ye, Liqun

Source: In Chemical Engineering Journal 15 April 2024 486

Highly selective formation of CO from domestic wastewater with Zero CO2 emissions through solar energy catalysis

Authors: Shi, Zhonglian, Li, Chao, Huang, Niu, Jiang, Ziyi, Wang, Li, Huang, Yingping, Kong, Xin Ying, Wong, Po Keung, Ye, Liqun

Source: In Applied Catalysis B: Environment and Energy April 2024 343

Emerging covalent triazine framework-based nanomaterials for electrochemical energy storage and conversion

Authors: Zheng, Yong, Khan, Niaz Ali, Ni, Xuepeng, Zhang, Kai A. I., Shen, Yi, Huang, Niu, Kong, Xin Ying, Ye, Liqun

Source: Chemical communications. 59(42):6314-6334

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183687562.0x000001&indx=1&recIds=ETOCvdc_100183687562.0x000001

Peroxide-mediated selective conversion of biomass polysaccharides over high entropy sulfides via solar energy catalysisElectronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d2ee03357g

Authors: Xu, Yixue, Wang, Li, Shi, Zhonglian, Su, Na, Li, Chao, Huang, Yingping, Huang, Niu, Deng, Yu, Li, Hui, Ma, Tianyi, Kong, Xin Ying, Lin, Wenjing, Zhou, Ying, Ye, Liqun

Source: Energy & environmental science. 16(4):1531-1539

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100179211101.0x000001&indx=1&recIds=ETOCvdc_100179211101.0x000001

Glucose-induced CRL4COP1-p53 axis amplifies glycometabolism to drive tumorigenesis

Authors: Su, Yang, Luo, Yifan, Zhang, Peitao, Lin, Hong, Pu, Weijie, Zhang, Hongyun, Wang, Huifang, Hao, Yi, Xiao, Yihang, Zhang, Xiaozhe, Wei, Xiayun, Nie, Siyue, Zhang, Keren, Fu, Qiuyu, Chen, Hao, Huang, Niu, Ren, Yan, Wu, Mingxuan, Chow, Billy Kwok Chong, Chen, Xing, Jin, Wenfei, Wang, Fengchao, Zhao, Li, Rao, Feng

Source: In Molecular Cell 6 July 2023 83(13):2316-2331

Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening

Authors: Zhu, Hui, Yang, Jincai, Huang, Niu

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 62(22):5485-5502

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632699812&indx=1&recIds=ETOCRN632699812

Ultradurable fluorinated V2AlC for peroxymonosulfate activation in organic pollutant degradation processes

Authors: Li, Chao, Song, Chenjie, Li, Hui, Ye, Liqun, Xu, Yixue, Huang, Yingping, Nie, Gongzhe, Zhang, Rumeng, Liu, Wei, Huang, Niu, Wong, Po Keung, Ma, Tianyi

Source: Chinese journal of catalysis. 43(7):1927-1936

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100166968516.0x000001&indx=1&recIds=ETOCvdc_100166968516.0x000001

AQ-coupled few-layered g-C3N4 nanoplates obtained by one-step mechanochemical treatment for efficient visible-light photocatalytic H2O2 production

Authors: Liu, Wei, Xu, Run, Wang, Yongye, Huang, Niu, Shimada, Toshihiro, Ye, Liqun

Source: International journal of hydrogen energy. 47(36):16005-16013

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100165297987.0x000001&indx=1&recIds=ETOCvdc_100165297987.0x000001

Pyrazole-containing pharmaceuticals: target, pharmacological activity, and their SAR studies

Authors: Li, Guangchen, Cheng, Yifu, Han, Chi, Song, Chun, Huang, Niu, Du, Yunfei

Source: RSC medicinal chemistry. 13(11):1300-1321

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164886126.0x000001&indx=1&recIds=ETOCvdc_100164886126.0x000001

Photosynthesis of Hydrogen and Its Synchronous Application in a Hydrogen Fuel Cell: A Comprehensive Experiment in the Undergraduate Teaching Laboratory

Authors: Huang, Niu, Li, Chao, Gan, Shili, Le, Cancan, Liu, Huan, Liu, Wei, Ye, Liqun

Source: Journal of chemical education. 99(9):3283-3288

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN630274908&indx=1&recIds=ETOCRN630274908

Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight

Authors: Xu, Kai, Zhang, Jinxiao, Duan, Xiaohui, Wan, Xiaobo, Huang, Niu, Schmidt, Bertil, Liu, Weiguo, Yang, Guangwen

Source: IEEE transactions on parallel and distributed systems. 33(12):4458-4471

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100158804822.0x000001&indx=1&recIds=ETOCvdc_100158804822.0x000001

Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1

Authors: Li, Linjie, Liao, Hanyi, Meng, Yumin, Li, Weiwei, Han, Pengcheng, Liu, Kefang, Wang, Qing, Li, Dedong, Zhang, Yanfang, Wang, Liang, Fan, Zheng, Zhang, Yuqin, Wang, Qiyue, Zhao, Xin, Sun, Yeping, Huang, Niu, Qi, Jianxun, Gao, George Fu

Source: In Cell 4 August 2022 185(16):2952-2960

Atomically dispersed antimony on N-doped carbon for highly efficient oxygen reduction reaction

Authors: Zhang, Dan, Xie, Xing, Sun, Panpan, Wei, Yongan, Gong, Tao, Huang, Niu, Lv, Xiaowei, Fang, Liang, Sun, Xiaohua

Source: In Chemical Engineering Journal 1 July 2022 439

Organic-inorganic hybrid hydrogel electrolyte for high-performance quasi-solid-state zinc-air batteries.

Authors: Wu, Mingzhu, Huang, Niu, Lv, Minghui, Wang, Fengyi, Ma, Fang, Deng, Yihan, Sun, Panpan, Zheng, Yong, Liu, Wei, Ye, Liqun

Source: Frontiers of Chemical Science & Engineering; Mar2025, Vol. 19 Issue 3, p1-11, 11p

Assessing small molecule conformational sampling methods in molecular docking.

Authors: Xia, Qiancheng^1,2, Fu, Qiuyu², Shen, Cheng², Brenk, Ruth³, Huang, Niu^1,2, huangniu@nibs.ac.cn

Source: Journal of Computational Chemistry; 1/5/2025, Vol. 46 Issue 1, p1-15, 15p

In-Situ derived Co1-xS@nitrogen-doped carbon nanoneedle array as a bifunctional electrocatalyst for flexible Zinc-air battery

Authors: Yan, Shufang, Luo, Chan, Zhang, Han, Yang, Liu, Huang, Niu, Zhang, Mingyi, Yu, Haihu, Sun, Panpan, Wang, Liping, Lv, Xiaowei, Sun, Xiaohua

Source: In Journal of Electroanalytical Chemistry 1 November 2021 900