Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. - Kuan Pern Tan; Thanh Binh Nguyen 007; Siddharth Patel; Raghavan Varadarajan; Mallur S. Madhusudhan (Nucleic Acids Res., 2013)

ThermoMutDB: a thermodynamic database for missense mutations. - Joicymara S. Xavier; Thanh-Binh Nguyen 007; Malancha Karmarkar; Stephanie Portelli; Pâmela M. Rezende; João P. L. Velloso; David B. Ascher; Douglas E. V. Pires (Nucleic Acids Res., 2021)

CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function. - Thanh-Binh Nguyen 007; Douglas E. V. Pires; David B. Ascher (Briefings Bioinform., 2022)

Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures. - Qisheng Pan; Thanh-Binh Nguyen 007; David B. Ascher; Douglas E. V. Pires (Briefings Bioinform., 2022)

Characterization on the oncogenic effect of the missense mutations of p53 via machine learning. - Qisheng Pan; Stephanie Portelli; Thanh-Binh Nguyen 007; David B. Ascher (Briefings Bioinform., 2023)