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Comprehensive classification of TP53 somatic missense variants based on their impact on p53 structural stability Journal article
Benjamin Tam, Philip Naderev P. Lagniton, Mariano da Luz, Bojin Zhao, Siddharth Sinha, Chon Lok Lei, San Ming Wang. Comprehensive classification of TP53 somatic missense variants based on their impact on p53 structural stability[J]. Briefings in Bioinformatics, 2024, 25(5), bbae400.
Authors:  Benjamin Tam;  Philip Naderev P. Lagniton;  Mariano da Luz;  Bojin Zhao;  Siddharth Sinha; et al.
Favorite | TC[WOS]:0 TC[Scopus]:0  IF:6.8/7.9 | Submit date：2024/08/07
Ramachandran Plot  Molecular Dynamics Simulations  Tp53  Somatic Missense Variants  
Classification of PTEN missense VUS through exascale simulations Journal article
Sinha, Siddharth, Li, Jiaheng, Tam, Benjamin, Wang, San Ming. Classification of PTEN missense VUS through exascale simulations[J]. Briefings in Bioinformatics, 2023, 24(6), bbad361.
Authors:  Sinha, Siddharth;  Li, Jiaheng;  Tam, Benjamin;  Wang, San Ming
Favorite | TC[WOS]:1 TC[Scopus]:1  IF:6.8/7.9 | Submit date：2023/12/04
Evolution Selection  Lipid Phosphatase Activity  Md Simulations  Pten  Replica Exchange Molecular Dynamics (Remd) Simulations  Variants Of Uncertain Significance (Vus)  
DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS Journal article
Lagniton,Philip Naderev P., Tam,Benjamin, Wang,San Ming. DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS[J]. Computer Methods and Programs in Biomedicine, 2023, 238, 107596.
Authors:  Lagniton,Philip Naderev P.;  Tam,Benjamin;  Wang,San Ming
Favorite | TC[WOS]:0 TC[Scopus]:0  IF:4.9/5.5 | Submit date：2023/08/03
Dihedral Angles  Human Muty Homolog (Mutyh)  Missense Variants  Molecular Dynamics Simulations (Md Simulations)  Protein Structure  Ramachandran Principle  Tumor Protein 53 (Tp53)  
Unravelling the dissolution dynamics of silicate minerals by deep learning molecular dynamics simulation: A case of dicalcium silicate Journal article
Yunjian Li, Hui Pan, Zongjin Li. Unravelling the dissolution dynamics of silicate minerals by deep learning molecular dynamics simulation: A case of dicalcium silicate[J]. CEMENT AND CONCRETE RESEARCH, 2023, 165, 107092.
Authors:  Yunjian Li;  Hui Pan;  Zongjin Li
Favorite | TC[WOS]:9 TC[Scopus]:9  IF:10.9/14.4 | Submit date：2023/04/03
Ab Initio Molecular Dynamics Simulations  Deep Neural Network Potential  Dicalcium Silicate  Dissolution  Thermodynamics And Kinetics  
Near-infrared fluorophores with absolute aggregation-caused quenching and negligible fluorescence re-illumination for in vivo bioimaging of nanocarriers Journal article
Cai, Yifan, Ji, Xin, Zhang, Yunsen, Liu, Chang, Zhang, Zichen, Lv, Yongjiu, Dong, Xiaochun, He, Haisheng, Qi, Jianping, Lu, Yi, Ouyang, Defang, Zhao, Weili, Wu, Wei. Near-infrared fluorophores with absolute aggregation-caused quenching and negligible fluorescence re-illumination for in vivo bioimaging of nanocarriers[J]. Aggregate, 2022.
Authors:  Cai, Yifan;  Ji, Xin;  Zhang, Yunsen;  Liu, Chang;  Zhang, Zichen; et al.
Favorite | TC[WOS]:30 TC[Scopus]:27 | Submit date：2024/01/10
Absolute Aggregation-caused Quenching  Aza-bodipy  Fluorescence Bioimaging  Fluorescence Re-illumination  Molecular Dynamics Simulations  Nanocarriers  Near-infrared  
Applications of Molecular Dynamics Simulation in Protein Study Review article
2022
Authors:  Sinha, Siddharth;  Tam, Benjamin;  Wang, San Ming
Favorite | TC[WOS]:32 TC[Scopus]:37  IF:3.3/3.6 | Submit date：2022/10/06
Molecular Dynamics Simulations  Enhanced Sampling Techniques  Membrane Dynamics  Gpcrs  Lipid-protein Interactions  Ace-2 Membrane Receptor  
Mechanistic insights into the clinical Y96D mutation with acquired resistance to AMG510 in the KRASG12C Journal article
Zhuang, Haiming, Fan, Jigang, Li, Mingyu, Zhang, Hao, Yang, Xiuyan, Lin, Ligen, Lu, Shaoyong, Wang, Qing, Liu, Yaqin. Mechanistic insights into the clinical Y96D mutation with acquired resistance to AMG510 in the KRASG12C[J]. Frontiers in Oncology, 2022, 12, 915512.
Authors:  Zhuang, Haiming;  Fan, Jigang;  Li, Mingyu;  Zhang, Hao;  Yang, Xiuyan; et al.
Favorite | TC[WOS]:7 TC[Scopus]:6  IF:3.5/4.0 | Submit date：2022/09/07
Amg510  Drug Resistance  G12c  Kras  Molecular Dynamics Simulations  
Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations Journal article
Sinha, Siddharth, Qin, Zixin, Tam, Benjamin, Wang, San Ming. Identification of deleterious variants of uncertain significance in BRCA2 BRC4 repeat through molecular dynamics simulations[J]. Briefings in functional genomics, 2022, 21(3), 202-215.
Authors:  Sinha, Siddharth;  Qin, Zixin;  Tam, Benjamin;  Wang, San Ming
Favorite | TC[WOS]:4 TC[Scopus]:4  IF:2.5/3.4 | Submit date：2022/06/10
Brca2 Brc4  Auc  Deleterious  Molecular Dynamics Simulations  Pca  Roc  Tolerated  Vus Classification  
An integrated computational methodology with data-driven machine learning, molecular modeling and PBPK modeling to accelerate solid dispersion formulation design Journal article
Gao,Hanlu, Wang,Wei, Dong,Jie, Ye,Zhuyifan, Ouyang,Defang. An integrated computational methodology with data-driven machine learning, molecular modeling and PBPK modeling to accelerate solid dispersion formulation design[J]. European Journal of Pharmaceutics and Biopharmaceutics, 2021, 158, 336-346.
Authors:  Gao,Hanlu;  Wang,Wei;  Dong,Jie;  Ye,Zhuyifan;  Ouyang,Defang
Favorite | TC[WOS]:35 TC[Scopus]:46  IF:4.4/4.8 | Submit date：2021/03/02
Dissolution Profile  Machine Learning  Molecular Dynamics (Md) Simulations  Pharmacokinetic Modeling  Solid Dispersion  
Solvation structure and molecular interactions of ibuprofen with ethanol and water: A theoretical study Journal article
Zhang,Mao, Huang,Yiping, Hao,Dule, Ji,Yuanhui, Ouyang,Defang. Solvation structure and molecular interactions of ibuprofen with ethanol and water: A theoretical study[J]. Fluid Phase Equilibria, 2020, 510, 112454.
Authors:  Zhang,Mao;  Huang,Yiping;  Hao,Dule;  Ji,Yuanhui;  Ouyang,Defang
Favorite | TC[WOS]:25 TC[Scopus]:27  IF:2.8/2.5 | Submit date：2021/03/02
Hydrogen Bonds  Ibuprofen  Interactions  Molecular Dynamics Simulations  Solvents