Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates. - Jenn-Huei Lii; Buyong Ma; Norman L. Allinger (J. Comput. Chem., 1999)

Molecular polarizabilities and induced dipole moments in molecular mechanics. - Buyong Ma; Jenn-Huei Lii; Norman L. Allinger (J. Comput. Chem., 2000)

A hierarchical, building-block-based computational scheme for protein structure prediction. - Chung-Jung Tsai; Buyong Ma; Yuk Yin Sham; Sandeep Kumar; Haim J. Wolfson; Ruth Nussinov (IBM J. Res. Dev., 2001)

Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR. - Zengjian Hu; Donnell Bowen; William M. Southerland; Antonio del Sol; Yongping Pan; Ruth Nussinov; Buyong Ma (PLoS Comput. Biol., 2007)

Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein. - Ping Zhou; Ning Zhang; Ruth Nussinov; Buyong Ma (J. Comput. Biol., 2015)

Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization. - Liang Xu; Shengsheng Shan; Yonggang Chen; Xiaojuan Wang; Ruth Nussinov; Buyong Ma (J. Chem. Inf. Model., 2015)

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm. - Rudy Clausen; Buyong Ma; Ruth Nussinov; Amarda Shehu (PLoS Comput. Biol., 2015)

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. - Tatiana Maximova; Ryan Moffatt; Buyong Ma; Ruth Nussinov; Amarda Shehu (PLoS Comput. Biol., 2016)

Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics. - Kazi Lutful Kabir; Ruth Nussinov; Buyong Ma; Amarda Shehu (BIBM, 2021)

REMD simulations of conformational dynamics of disordered nuclear localization signal peptide of p53 protein. - Linghao Zhang; Ganggang Bai; Honglin Xu; Jingjing Li; Buyong Ma (Commun. Inf. Syst., 2024)

GATRsite: RNA-Ligand Binding Site Prediction Using Graph Attention Networks and Pretrained RNA Language Models. - Chuance Sun; Linghao Zhang; Lingfeng Zhang; Yuehua Song; Buyong Ma; Yanjing Wang 003 (J. Chem. Inf. Model., 2025)