Dynamics of large proteins through hierarchical levels of coarse-grained structures. - Pemra Doruker; Robert L. Jernigan; Ivet Bahar (J. Comput. Chem., 2002)

Mimicking Protein Dynamics by the Integration of Elastic Network Model with Time Series Analysis. - Burak Alakent; Mehmet C. Camurdan; Pemra Doruker (Int. J. High Perform. Comput. Appl., 2007)

Effect of ligand binding on the intraminimum dynamics of proteins. - Burak Alakent; Sena Baskan; Pemra Doruker (J. Comput. Chem., 2011)

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

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase. - Zeynep Kurkcuoglu; Pemra Doruker (Entropy, 2013)

Protein-Ligand Complexes as Constrained Dynamical Systems. - Burak T. Kaynak; Pemra Doruker (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)

Predicting allosteric pockets in protein biological assemblages. - Ambuj Kumar; Burak T. Kaynak; Karin S. Dorman; Pemra Doruker; Robert L. Jernigan (Bioinform., 2023)