Structural Modeling of Protein Interactions by Analogy: Application to PSD-95. - Dmitry Korkin; Fred P. Davis; Frank Alber; Tinh Luong; Min-Yi Shen; Vladan Lucic; Mary B. Kennedy; Andrej Sali (PLoS Comput. Biol., 2006)

A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II. - Shirley Pepke; Tamara Kinzer-Ursem; Stefan Mihalas; Mary B. Kennedy (PLoS Comput. Biol., 2010)

Multi-state Modeling of Biomolecules. - Melanie I. Stefan; Thomas M. Bartol; Terrence J. Sejnowski; Mary B. Kennedy (PLoS Comput. Biol., 2014)

A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation. - Matthew C. Pharris; Neal M. Patel; Tyler G. VanDyk; Thomas M. Bartol; Terrence J. Sejnowski; Mary B. Kennedy; Melanie I. Stefan; Tamara Kinzer-Ursem (PLoS Comput. Biol., 2019)

Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. - Mariam Ordyan; Tom Bartol; Mary B. Kennedy; Padmini Rangamani; Terrence J. Sejnowski (PLoS Comput. Biol., 2020)

MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. - Adam Husár; Mariam Ordyan; Guadalupe C. Garcia; Joel G. Yancey; Ali Sinan Saglam; James R. Faeder; Thomas M. Bartol; Mary B. Kennedy; Terrence J. Sejnowski (PLoS Comput. Biol., 2024)