New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue. - Olivia Wise; Orkid Coskuner (J. Comput. Chem., 2014)

Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins. - Orkid Coskuner; Vladimir N. Uversky (J. Chem. Inf. Model., 2017)

Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β42. - Orkid Coskuner-Weber; Vladimir N. Uversky (J. Chem. Inf. Model., 2019)

Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies. - Birgit Strodel; Orkid Coskuner-Weber (J. Chem. Inf. Model., 2019)

Key genes and pathways in the molecular landscape of pancreatic ductal adenocarcinoma: A bioinformatics and machine learning study. - Sinan Eyuboglu; Semih Alpsoy; Vladimir N. Uversky; Orkid Coskuner-Weber (Comput. Biol. Chem., 2024)

Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing. - Orkid Coskuner-Weber; Semih Alpsoy; Ozgur Yolcu; Egehan Teber; Ario de Marco; Spase Shumka (Comput. Biol. Chem., 2025)

Effects of pathological mutations on the CHCHD2 monomer structure: A study by AlphaFold3 linked to the generation of conformational ensembles. - Zeyneb Azra Özmen; Fatma Nilsu Çayli; Vladimir N. Uversky; Junga Alexa Woo; David E. Kang; Orkid Coskuner-Weber (Comput. Biol. Medicine, 2025)