Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments. - Ahmet Bakan; Ivet Bahar (Pacific Symposium on Biocomputing, 2011)

ProDy: Protein Dynamics Inferred from Theory and Experiments. - Ahmet Bakan; Lidio M. C. Meireles; Ivet Bahar (Bioinform., 2011)

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics. - Zeynep Kurkcuoglu; Ahmet Bakan; Duygu Kocaman; Ivet Bahar; Pemra Doruker (PLoS Comput. Biol., 2012)

Evol and ProDy for bridging protein sequence evolution and structural dynamics. - Ahmet Bakan; Anindita Dutta; Wenzhi Mao; Ying Liu; Chakra Chennubhotla 001; Timothy R. Lezon; Ivet Bahar (Bioinform., 2014)