Why Amantadine Loses Its Function in Influenza M2 Mutants: MD Simulations. - Chittima Laohpongspaisan; Thanyada Rungrotmongkol; Pathumwadee Intharathep; Maturos Malaisree; Panita Decha; Ornjira Aruksakunwong; Pornthep Sompornpisut; Supot Hannongbua (J. Chem. Inf. Model., 2009)

Dynamic Behavior of Avian Influenza A Virus Neuraminidase Subtype H5N1 in Complex with Oseltamivir, Zanamivir, Peramivir, and Their Phosphonate Analogues. - Thanyarat Udommaneethanakit; Thanyada Rungrotmongkol; Urban Bren; Vladimir Frecer; Stanislav Miertus (J. Chem. Inf. Model., 2009)

Evolution of Human Receptor Binding Affinity of H1N1 Hemagglutinins from 1918 to 2009 Pandemic Influenza A Virus. - Nadtanet Nunthaboot; Thanyada Rungrotmongkol; Maturos Malaisree; Nopporn Kaiyawet; Panita Decha; Pornthep Sompornpisut; Yong Poovorawan; Supot Hannongbua (J. Chem. Inf. Model., 2010)

Molecular Dynamic Behavior and Binding Affinity of Flavonoid Analogues to the Cyclin Dependent Kinase 6/cyclin D Complex. - Wasinee Khuntawee; Thanyada Rungrotmongkol; Supot Hannongbua (J. Chem. Inf. Model., 2012)

Effect of Halogen Substitutions on dUMP to Stability of Thymidylate Synthase/dUMP/mTHF Ternary Complex Using Molecular Dynamics Simulation. - Nopporn Kaiyawet; Thanyada Rungrotmongkol; Supot Hannongbua (J. Chem. Inf. Model., 2013)

Key Binding and Susceptibility of NS3/4A Serine Protease Inhibitors against Hepatitis C Virus. - Arthitaya Meeprasert; Supot Hannongbua; Thanyada Rungrotmongkol (J. Chem. Inf. Model., 2014)

Molecular Dynamics Simulations of the Interaction of Beta Cyclodextrin with a Lipid Bilayer. - Wasinee Khuntawee; Peter Wolschann; Thanyada Rungrotmongkol; Jirasak Wong-ekkabut; Supot Hannongbua (J. Chem. Inf. Model., 2015)

Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study. - Jiraphorn Phanich; Thanyada Rungrotmongkol; Nawee Kungwan; Supot Hannongbua (J. Comput. Aided Mol. Des., 2016)

Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics. - Wasinee Khuntawee; Manaschai Kunaseth; Chompoonut Rungnim; Suradej Intagorn; Peter Wolschann; Nawee Kungwan; Thanyada Rungrotmongkol; Supot Hannongbua (J. Chem. Inf. Model., 2017)

Theoretical and Experimental Studies on Inclusion Complexes of Pinostrobin and β-Cyclodextrins. - Jintawee Kicuntod; Kanyani Sangpheak; Monika Müller; Peter Wolschann; Helmut Viernstein; Saeko Yanaka; Koichi Kato; Warinthorn Chavasiri; Piamsook Pongsawasdi; Nawee Kungwan; Thanyada Rungrotmongkol (Sensors, 2018)

Understanding of the drug resistance mechanism of hepatitis C virus NS3/4A to paritaprevir due to D168N/Y mutations: A molecular dynamics simulation perspective. - Thitiya Boonma; Bodee Nutho; Thanyada Rungrotmongkol; Nadtanet Nunthaboot (Comput. Biol. Chem., 2019)

Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. - Chonnikan Hanpaibool; Matina Leelawiwat; Kaito Takahashi; Thanyada Rungrotmongkol (J. Comput. Aided Mol. Des., 2020)

In silico and in vitro anti-AChE activity investigations of constituents from Mytragyna speciosa for Alzheimer's disease treatment. - Wansiri Innok; Asadhawut Hiranrat; Netnapa Chana; Thanyada Rungrotmongkol; Panita Kongsune (J. Comput. Aided Mol. Des., 2021)

Insights into binding molecular mechanism of hemagglutinin H3N2 of influenza virus complexed with arbidol and its derivative: A molecular dynamics simulation perspective. - Thitiya Boonma; Nattharuja Soikudrua; Bodee Nutho; Thanyada Rungrotmongkol; Nadtanet Nunthaboot (Comput. Biol. Chem., 2022)

Structural dynamics and kinase inhibitory activity of three generations of tyrosine kinase inhibitors against wild-type, L858R/T790M, and L858R/T790M/C797S forms of EGFR. - Duangjai Todsaporn; Panupong Mahalapbutr; Rungtiva P. Poo-arporn; Kiattawee Choowongkomon; Thanyada Rungrotmongkol (Comput. Biol. Medicine, 2022)

Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease. - Kowit Hengphasatporn; Patcharin Wilasluck; Peerapon Deetanya; Kittikhun Wangkanont; Warinthorn Chavasiri; Peerapat Visitchanakun; Asada Leelahavanichkul; Wattamon Paunrat; Siwaporn Boonyasuppayakorn; Thanyada Rungrotmongkol; Supot Hannongbua; Yasuteru Shigeta (J. Chem. Inf. Model., 2022)

Structure-based virtual screening for potent inhibitors of GH-20 β-N-acetylglucosaminidase: Classical and machine learning scoring functions, and molecular dynamics simulations. - Grittin Phengsakun; Bundit Boonyarit; Thanyada Rungrotmongkol; Wipa Suginta (Comput. Biol. Chem., 2023)

Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CLpro through Structure-Based Virtual Screening and Experimental Approaches. - Piyatida Pojtanadithee; Kowit Hengphasatporn; Aphinya Suroengrit; Siwaporn Boonyasuppayakorn; Patcharin Wilasluck; Peerapon Deetanya; Kittikhun Wangkanont; I. Putu Sukanadi; Warinthorn Chavasiri; Peter Wolschann; Thierry Langer; Yasuteru Shigeta; et al. (J. Chem. Inf. Model., 2023)

Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation. - Chonnikan Hanpaibool; Puey Ounjai; Sirilata Yotphan; Adrian J. Mulholland; James Spencer; Natharin Ngamwongsatit; Thanyada Rungrotmongkol (J. Comput. Aided Mol. Des., 2023)

Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation. - Saba Ali; Aamir Aman; Kowit Hengphasatporn; Lipika Oopkaew; Bunyaporn Todee; Ryo Fujiki; Ryuhei Harada; Yasuteru Shigeta; Kuakarun Krusong; Kiattawee Choowongkomon; Warinthorn Chavasiri; Peter Wolschann; et al. (Comput. Biol. Chem., 2024)

GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity. - Bundit Boonyarit; Nattawin Yamprasert; Pawit Kaewnuratchadasorn; Jiramet Kinchagawat; Chanatkran Prommin; Thanyada Rungrotmongkol; Sarana Nutanong (J. Comput. Chem., 2024)

Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery. - Hathaichanok Chuntakaruk; Kajjana Boonpalit; Jiramet Kinchagawat; Fahsai Nakarin; Tanatorn Khotavivattana; Chanat Aonbangkhen; Yasuteru Shigeta; Kowit Hengphasatporn; Sarana Nutanong; Thanyada Rungrotmongkol; Supot Hannongbua (J. Comput. Chem., 2024)

Exploring mimosamycin as a Janus kinase 2 inhibitor: A combined computational and experimental investigation. - Kamonpan Sanachai; Kowit Hengphasatporn; Supakarn Chamni; Khanit Suwanborirux; Panupong Mahalapbutr; Yasuteru Shigeta; Supaporn Seetaha; Kiattawee Choowongkomon; Thanyada Rungrotmongkol (Comput. Biol. Chem., 2025)

Rational Design for Antioxidant Diphenylamine Derivatives Using Quantitative Structure-Activity Relationships and Quantum Mechanics Calculations. - Ayokanmi Joseph Aremu; Phiphob Naweephattana; Ismail Dwi Putra; Borwornlak Toopradab; Phornphimon Maitarad; Thanyada Rungrotmongkol (J. Comput. Chem., 2025)

Pre-training strategy for antiviral drug screening with low-data graph neural network: A case study in HIV-1 K103N reverse transcriptase. - Kajjana Boonpalit; Hathaichanok Chuntakaruk; Jiramet Kinchagawat; Peter Wolschann; Supot Hannongbua; Thanyada Rungrotmongkol; Sarana Nutanong (J. Comput. Chem., 2025)

Theoretical investigation of structure and electronic properties in Cisplatin-citrate complexes. - Lipika Oopkaew; Yuwanda Injongkol; Nawee Kungwan; Thanyada Rungrotmongkol (J. Comput. Chem., 2025)

M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy. - Nalini Schaduangrat; Hathaichanok Chuntakaruk; Thanyada Rungrotmongkol; Pakpoom Mookdarsanit; Watshara Shoombuatong (BMC Bioinform., 2025)