DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates. - Ignacia Echeverria; Garegin A. Papoian (PLoS Comput. Biol., 2015)

MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks. - Konstantin Popov; James Komianos; Garegin A. Papoian (PLoS Comput. Biol., 2016)

Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling. - Aravind Chandrasekaran; Arpita Upadhyaya; Garegin A. Papoian (PLoS Comput. Biol., 2019)

AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. - Shikai Jin; Vinícius G. Contessoto; Mingchen Chen; Nicholas P. Schafer; Wei Lu; Xun Chen; Carlos Bueno; Arya Hajitaheri; Brian J. Sirovetz; Aram Davtyan; Garegin A. Papoian; Min-Yeh Tsai; et al. (Nucleic Acids Res., 2020)

Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry. - Xiaona Li; Qin Ni; Xiuxiu He; Jun Kong 002; Soon-Mi Lim; Garegin A. Papoian; Jerome P. Trzeciakowski; Andreea Trache; Yi Jiang (PLoS Comput. Biol., 2020)

Simulated actin reorganization mediated by motor proteins. - Maria-Veronica Ciocanel; Aravind Chandrasekaran; Carli Mager; Qin Ni; Garegin A. Papoian; Adriana T. Dawes (PLoS Comput. Biol., 2022)

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. - Haiqing Zhao; Hao Wu; Alex Guseman; Dulith Abeykoon; Christina M. Camara; Yamini Dalal; David Fushman; Garegin A. Papoian (PLoS Comput. Biol., 2024)

Energy Landscapes and Structural Plasticity of Intrinsically Disordered Histones. - Rafael Giordano Viegas; Hao Wu; Murilo Nogueira Sanches; Garegin A. Papoian; Vitor B. P. Leite (J. Chem. Inf. Model., 2025)