Accurate Determination of Host-Guest Standard Binding Free Energies and Kinetic Parameters from Replica Exchange Molecular Dynamics Simulation.

Jinan Wang

Leyun Wu Zijian Han Zhaoyin Zhou Jinan Wang Weiliang Zhu Zhijian Xu Accurate Determination of Host-Guest Standard Binding Free Energies and Kinetic Parameters from Replica Exchange Molecular Dynamics Simulation. 2026 5345-5356 66 J. Chem. Inf. Model. 9 https://doi.org/10.1021/acs.jcim.5c02914 db/journals/jcisd/jcisd66.html#WuHZWZX26 streams/journals/jcisd

Hua Zhong Yan Zhang Guanbin Zhu Xiaoli Zheng Jinan Wang Jianghe Kang Ziying Lin Xin Yue Preoperative prediction of microvascular invasion and relapse-free survival in hepatocellular Carcinoma ≥3 cm using CT radiomics: Development and external validation. 141 2025 December 25 BMC Medical Imaging 1 https://doi.org/10.1186/s12880-025-01677-2 db/journals/bmcmi/bmcmi25.html#ZhongZZZWKLY25 streams/journals/bmcmi

David A. Case David S. Cerutti Vinícius Wilian D. Cruzeiro Thomas A. Darden Robert E. Duke Mahdieh Ghazimirsaeed George M. Giambasu Timothy J. Giese Andreas W. Götz Julie A. Harris Koushik Kasavajhala Tai-Sung Lee Zhen Li 0038 Charles Lin Jian Liu 0019 Yinglong Miao Romelia Salomón-Ferrer Jana Shen Ryan Snyder Jason M. Swails Ross C. Walker Jinan Wang Xiongwu Wu Jinzhe Zeng Thomas E. Cheatham III Daniel R. Roe Adrian E. Roitberg Carlos Simmerling Darrin M. York Maria C. Nagan Kenneth M. Merz Jr. Recent Developments in Amber Biomolecular Simulations. 7835-7843 2025 65 J. Chem. Inf. Model. 15 https://doi.org/10.1021/acs.jcim.5c01063 db/journals/jcisd/jcisd65.html#CaseCCDDGGGGHKLLLLMSSSS25 streams/journals/jcisd

Xiangrong Zhuang Jinan Wang Jianghe Kang Ziying Lin Diagnosis of Acute Versus Chronic Thoracolumbar Vertebral Compression Fractures Using CT Radiomics Based on Machine Learning: a Preliminary Study. 2183-2193 2025 38 J. Imaging Inform. Medicine 4 https://doi.org/10.1007/s10278-024-01359-5 db/journals/jdi/jdi38.html#ZhuangWKL25 streams/journals/jdi

Wenjing Wang Liang Liu 0006 Kaibin Zhang Keyue Yang Lingwei Kuang Ziyi Zheng Jinan Wang Junliang Cao NPAC: numeric pattern aware compression algorithm for floating-point time-series data. 69 2025 November 28 World Wide Web (WWW) 6 https://doi.org/10.1007/s11280-025-01382-8 db/journals/www/www28.html#WangLZYKZWC25 streams/journals/www

Hua Zhong Qianwen Huang Xiaoli Zheng Yong Wang Yanan Qian Xingbiao Chen Jinan Wang Shaoyin Duan Generation of virtual monoenergetic images at 40 keV of the upper abdomen and image quality evaluation based on generative adversarial networks. 151 2024 December 24 BMC Medical Imaging 1 https://doi.org/10.1186/s12880-024-01331-3 db/journals/bmcmi/bmcmi24.html#ZhongHZWQCWD24

Sana Akhter Zhichao Tang Jinan Wang Mercy Haboro Erik D. Holmstrom Jingxin Wang Yinglong Miao Mechanism of Ligand Binding to Theophylline RNA Aptamer. 1017-1029 2024 64 J. Chem. Inf. Model. 3 https://doi.org/10.1021/acs.jcim.3c01454 https://www.wikidata.org/entity/Q129881318 db/journals/jcisd/jcisd64.html#AkhterTWHHWM24

Timothy Hasse Esra Mantei Rezvan Shahoei Shristi Pawnikar Jinan Wang Yinglong Miao Yu-ming M. Huang Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein. 1011955 2024 20 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1011955 db/journals/ploscb/ploscb20.html#HasseMSPWMH24 streams/journals/ploscb

Xuebin Wang Taifu Wang Zhihao Xie Youjin Zhang Shiqiang Xia Ruixue Sun Xinqiu He Ruizhi Xiang Qiwen Zheng Zhencheng Liu Jinan Wang Honglong Wu Xiangqian Jin Weijun Chen Dongfang Li Zengquan He GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences. 2023 March 24 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbad092 db/journals/bib/bib24.html#WangWXZXSHXZLWWJCLH23

Apurba Bhattarai Jinan Wang Yinglong Miao G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State. 460-471 2020 41 J. Comput. Chem. 5 https://doi.org/10.1002/jcc.26082 https://www.wikidata.org/entity/Q90646236 db/journals/jcc/jcc41.html#BhattaraiWM20

Cheng Peng Jinan Wang Zhijian Xu Tingting Cai Weiliang Zhu Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge. 1773-1780 2020 41 J. Comput. Chem. 19 https://doi.org/10.1002/jcc.26218 https://www.wikidata.org/entity/Q94466251 db/journals/jcc/jcc41.html#PengWXCZ20

Zhaoqiang Chen Xinben Zhang Cheng Peng Jinan Wang Zhijian Xu Kaixian Chen Jiye Shi Weiliang Zhu D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. 3353-3358 2019 59 J. Chem. Inf. Model. 8 https://doi.org/10.1021/acs.jcim.9b00332 https://www.wikidata.org/entity/Q91551261 db/journals/jcisd/jcisd59.html#ChenZPWXCSZ19

Jinan Wang Zihu Guo Yingxue Fu 0002 Ziyin Wu Chao Huang 0030 Chunli Zheng Piar Ali Shar Zhenzhong Wang Wei Xiao Yonghua Wang Weak-binding molecules are not drugs? - toward a systematic strategy for finding effective weak-binding drugs. 321-332 2017 18 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbw018 https://www.wikidata.org/entity/Q38897226 db/journals/bib/bib18.html#WangGFWHZSWXW17

Peng Li 0004 Chao Huang 0030 Yingxue Fu 0002 Jinan Wang Ziyin Wu Jinlong Ru Chunli Zheng Zihu Guo Xuetong Chen Wei Zhou 0014 Wenjuan Zhang Yan Li 0025 Jianxin Chen Aiping Lu Yonghua Wang Large-scale exploration and analysis of drug combinations. 2007-2016 2015 31 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btv080 https://www.wikidata.org/entity/Q41455882 db/journals/bioinformatics/bioinformatics31.html#LiHFWWRZGCZZLCL15

Xin Liu Shaoliang Peng Canqun Yang Chengkun Wu Haiqiang Wang Qian Cheng Weiliang Zhu Jinan Wang mAMBER: Accelerating Explicit Solvent Molecular Dynamic with Intel Xeon Phi Many-Integrated Core Coprocessors. 729-732 2015 CCGRID https://doi.org/10.1109/CCGrid.2015.66 https://doi.ieeecomputersociety.org/10.1109/CCGrid.2015.66 conf/ccgrid/2015 db/conf/ccgrid/ccgrid2015.html#LiuPYWWCZW15 Haiqiang Wang Shaoliang Peng Xiaoqian Zhu Chengkun Wu Xin Liu Qian Chen Weiliang Zhu Jinan Wang Huaiyu Yang A Method to Accelerate GROMACS in Offload Mode on Tianhe-2 Supercomputer. 781-784 2015 CCGRID https://doi.org/10.1109/CCGrid.2015.65 https://doi.ieeecomputersociety.org/10.1109/CCGrid.2015.65 conf/ccgrid/2015 db/conf/ccgrid/ccgrid2015.html#WangPZWLCZWY15

Lihui Zhang Tianjun Liu Xia Wang Jinan Wang Guohui Li Yan Li 0025 Ling Yang Yonghua Wang Insight into the binding mode and the structural features of the pyrimidine derivatives as human A<sub>2A</sub> adenosine receptor antagonists. 13-22 2014 115 Biosyst. https://doi.org/10.1016/j.biosystems.2013.04.003 https://www.wikidata.org/entity/Q45698661 db/journals/biosystems/biosystems115.html#ZhangLWWLLYW14

Jinlong Ru Peng Li 0004 Jinan Wang Wei Zhou 0014 Bohui Li Chao Huang 0030 Pidong Li Zihu Guo Weiyang Tao Yinfeng Yang Xue Xu Yan Li 0025 Yonghua Wang Ling Yang TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. 13 2014 6 J. Cheminformatics 1 https://doi.org/10.1186/1758-2946-6-13 https://www.wikidata.org/entity/Q27703005 db/journals/jcheminf/jcheminf6.html#RuLWZLHLGTYXLWY14

Jing Lu Jianlong Peng Jinan Wang Qiancheng Shen Yi Bi Likun Gong Mingyue Zheng Xiaomin Luo Weiliang Zhu Hualiang Jiang Kaixian Chen Estimation of acute oral toxicity in rat using local lazy learning. 26 2014 6 J. Cheminformatics 1 https://doi.org/10.1186/1758-2946-6-26 https://www.wikidata.org/entity/Q33719719 db/journals/jcheminf/jcheminf6.html#LuPWSBGZLZJC14

Jianzhong Chen Jinan Wang Weiliang Zhu Guohui Li A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. 965-974 2013 27 J. Comput. Aided Mol. Des. 11 https://doi.org/10.1007/s10822-013-9693-z https://www.wikidata.org/entity/Q86826027 db/journals/jcamd/jcamd27.html#ChenWZL13

Xiuqin Huang Huimin Zhang Mengchen Li Jinan Wang Ying Zhang Ran Tao Mental Health, Personality, and Parental Rearing Styles of Adolescents with Internet Addiction Disorder. 401-406 2010 13 Cyberpsychology Behav. Soc. Netw. 4 https://doi.org/10.1089/cyber.2009.0222 https://www.wikidata.org/entity/Q49083503 db/journals/cbsn/cbsn13.html#XiuqinHMJYR10

Sana Akhter Apurba Bhattarai Yi Bi Tingting Cai Junliang Cao David A. Case David S. Cerutti Thomas E. CheathamThomas E. Cheatham III Jianxin Chen Jianzhong Chen Kaixian Chen Qian Chen Weijun Chen Xingbiao Chen Xuetong Chen Zhaoqiang Chen Qian Cheng Vinícius Wilian D. Cruzeiro Thomas A. Darden Shaoyin Duan Robert E. Duke Yingxue Fu 0002 Mahdieh Ghazimirsaeed George M. Giambasu Timothy J. Giese Likun Gong Andreas W. Götz Zihu Guo Mercy Haboro Zijian Han Julie A. Harris Timothy Hasse Xinqiu He Zengquan He Erik D. Holmstrom Chao Huang 0030 Qianwen Huang Xiuqin Huang Yu-ming M. Huang Hualiang Jiang Xiangqian Jin Jianghe Kang Koushik Kasavajhala Lingwei Kuang Tai-Sung Lee Bohui Li Dongfang Li GuoHui LiGuohui Li Mengchen Li Peng Li 0004 Pidong Li Yan Li 0025 Zhen Li 0038 Charles Lin Ziying Lin Jian Liu 0019 Liang Liu 0006 Tianjun Liu Xin Liu Zhencheng Liu Aiping Lu Jing Lu Xiaomin Luo Esra Mantei Kenneth M. Merz Jr. Yinglong Miao Maria C. Nagan Shristi Pawnikar Cheng Peng Jianlong Peng Shaoliang Peng Yanan Qian Daniel R. Roe Adrian E. Roitberg Jinlong Ru Romelia Salomón-Ferrer Rezvan Shahoei Piar Ali Shar Jana Shen Qiancheng Shen Jiye Shi Carlos Simmerling Ryan Snyder Ruixue Sun Jason M. Swails Zhichao Tang Ran Tao Weiyang Tao Ross C. Walker Haiqiang Wang Jingxin Wang Taifu Wang Wenjing Wang Xia Wang Xuebin Wang Yong Wang Yonghua Wang Zhenzhong Wang Chengkun Wu Honglong Wu Leyun Wu Xiongwu Wu Ziyin Wu Shiqiang Xia Ruizhi Xiang Wei Xiao Zhihao Xie Xue Xu Zhijian Xu Canqun Yang Huaiyu Yang Keyue Yang Ling Yang Yinfeng Yang Darrin M. York Xin Yue Jinzhe Zeng Huimin Zhang Kaibin Zhang Lihui Zhang Wenjuan Zhang Xinben Zhang Yan Zhang Ying Zhang Youjin Zhang Chunli Zheng Mingyue Zheng Qiwen Zheng Xiaoli Zheng Ziyi Zheng Hua Zhong Wei Zhou 0014 Zhaoyin Zhou Guanbin Zhu Weiliang Zhu Xiaoqian Zhu Xiangrong Zhuang