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Proteins|April 21, 2018
Structure refinement of membrane proteins via molecular dynamics simulationsBercem Dutagaci, Lim Heo, Michael FeigJournal of Chemical Information and Modeling|November 21, 2017
Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane ModelBercem Dutagaci, Michael FeigJournal of Computational Chemistry|February 5, 2017
Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helicesBercem Dutagaci, Maryam Sayadi, Michael FeigJournal of Chemical Theory and Computation|May 6, 2017
Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring FunctionsBercem Dutagaci, Kitiyaporn Wittayanarakul, Takaharu Mori, et al.The Journal of Physical Chemistry. B|November 28, 2022
Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte SolutionsPeter K Walhout, Zhe He, Bercem Dutagaci, et al.Plos Computational Biology|March 22, 2023
Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learningBercem Dutagaci, Bingbing Duan, Chenxi Qiu, et al.Journal of Chemical Information and Modeling|December 13, 2018
Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine LearningStephanie A Brocke, Alexandra Degen, Alexander D MacKerell, et al.Journal of Computer-Aided Molecular Design|November 21, 2023
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stabilityAdan Gallardo, Bercem DutagaciProteins|November 7, 2019
High-accuracy protein structures by combining machine-learning with physics-based refinementLim Heo, Michael FeigProceedings of the National Academy of Sciences of the United States of America|December 12, 2018
Experimental accuracy in protein structure refinement via molecular dynamics simulationsLim Heo, Michael FeigPageof 20