Structure, Dynamics and Solvation of HIV-1 Protease/Saquinavir Complex in Aqueous Solution and Their Contributions to Drug Resistance: Molecular Dynamic Simulations. - Kitiyaporn Wittayanarakul; Ornjira Aruksakunwong; Pornthep Sompornpisut; Vannajan Sanghiran Lee; Vudhichai Parasuk; Surapong Pinitglang; Supot Hannongbua (J. Chem. Inf. Model., 2005)

Molecular Dynamic and Free Energy Studies of Primary Resistance Mutations in HIV-1 Protease-Ritonavir Complexes. - Ornjira Aruksakunwong; Peter Wolschann; Supot Hannongbua; Pornthep Sompornpisut (J. Chem. Inf. Model., 2006)

On the correlation between drug-resistant pattern of HIV-1 protease inhibitors and binding free energy and structural changes. - Kitiyaporn Wittayanarakul; Supot Hannongbua; Michael Feig (BMC Syst. Biol., 2007)

Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. - Kitiyaporn Wittayanarakul; Supot Hannongbua; Michael Feig (J. Comput. Chem., 2008)

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)

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)

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)

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)

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)