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)