DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. - Pemra Ozbek; Seren Soner; Burak Erman; Turkan Haliloglu (Nucleic Acids Res., 2010)

DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. - Seren Soner; Pemra Ozbek; José Ignacio Garzón; Nir Ben-Tal; Turkan Haliloglu (PLoS Comput. Biol., 2015)

Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study. - Pemra Ozbek (Comput. Biol. Chem., 2016)

A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis. - Onur Serçinoglu; Gülin Özcan; Zeynep Kutlu Kabas; Pemra Ozbek (J. Comput. Aided Mol. Des., 2016)

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations. - Onur Serçinoglu; Pemra Ozbek (Nucleic Acids Res., 2018)

ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism. - Rasim Murat Aydinkal; Onur Serçinoglu; Pemra Ozbek (Nucleic Acids Res., 2019)

Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles. - Asuman Bunsuz; Onur Serçinoglu; Pemra Ozbek (Comput. Biol. Chem., 2020)

Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy. - Metin Yazar; Pemra Ozbek (J. Comput. Aided Mol. Des., 2020)

Differential Interactome Based Drug Repositioning Unraveled Abacavir, Exemestane, Nortriptyline Hydrochloride, and Tolcapone as Potential Therapeutics for Colorectal Cancers. - Hande Beklen; Sema Arslan; Gizem Gulfidan; Beste Turanli; Pemra Ozbek; Betül Karademir Yilmaz; Kazim Yalçin Arga (Frontiers Bioinform., 2021)

Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor-Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations. - Elif Naz Bingöl; Onur Serçinoglu; Pemra Ozbek (J. Chem. Inf. Model., 2021)

Assessment of 13 in silico pathogenicity methods on cancer-related variants. - Metin Yazar; Pemra Ozbek (Comput. Biol. Medicine, 2022)