Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. - Karolina Mikulska-Ruminska; Indira Shrivastava; James Krieger; She Zhang; Hongchun Li; Hülya Bayir; Sally E. Wenzel; Andrew P. Vandemark; Valerian E. Kagan; Ivet Bahar (J. Chem. Inf. Model., 2019)

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution. - Burak T. Kaynak; She Zhang; Ivet Bahar; Pemra Doruker (Bioinform., 2021)

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python. - She Zhang; James Krieger; Yan Zhang; Cihan Kaya; Burak T. Kaynak; Karolina Mikulska-Ruminska; Pemra Doruker; Hongchun Li; Ivet Bahar (Bioinform., 2021)

Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories. - She Zhang; Jeffrey P. Thompson; Junchao Xia; Anthony T. Bogetti; Forrest York; A. Geoffrey Skillman; Lillian T. Chong; David N. LeBard (J. Chem. Inf. Model., 2022)

Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow. - Omer Acar; She Zhang; Ivet Bahar; Anne-Ruxandra Carvunis (PLoS Comput. Biol., 2022)

Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRAS G12D. - Neha Vithani; She Zhang; Jeffrey P. Thompson; Lara A. Patel; Alex Demidov; Junchao Xia; Alexander Balaeff; Ahmet Mentes; Yelena A. Arnautova; Anna Kohlmann; J. David Lawson; Anthony Nicholls; et al. (J. Chem. Inf. Model., 2024)