Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats. - Amit Mor; Guy Ziv; Yaakov Levy (J. Comput. Chem., 2008)

Understanding hydrogen-bond patterns in proteins using network motifs. - Ofer Rahat; Uri Alon 001; Yaakov Levy; Gideon Schreiber (Bioinform., 2009)

Modulating Protein-DNA Interactions by Post-Translational Modifications at Disordered Regions. - Dana Vuzman; Yonit Hoffman; Yaakov Levy (Pacific Symposium on Biocomputing, 2012)

Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. - Arumay Pal; Yaakov Levy (PLoS Comput. Biol., 2019)

Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA. - Arumay Pal; Yaakov Levy (PLoS Comput. Biol., 2020)