Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices. - Bercem Dutagaci; Maryam Sayadi; Michael Feig (J. Comput. Chem., 2017)

Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model. - Bercem Dutagaci; Michael Feig (J. Chem. Inf. Model., 2017)

Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. - Stephanie A. Brocke; Alexandra Degen; Alexander D. MacKerell Jr.; Bercem Dutagaci; Michael Feig (J. Chem. Inf. Model., 2019)

Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations. - Adan Gallardo; Brandon M. Bogart; Bercem Dutagaci (J. Chem. Inf. Model., 2022)

Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning. - Bercem Dutagaci; Bingbing Duan; Chenxi Qiu; Craig D. Kaplan; Michael Feig (PLoS Comput. Biol., 2023)

Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability. - Adan Gallardo; Bercem Dutagaci (J. Comput. Aided Mol. Des., 2024)