2018
Butler, Brandon M., I. Can Kazan, Avishek Kumar, and S. Banu Ozkan. “Coevolving Residues Inform Protein Dynamics Profiles and Disease Susceptibility of NSNVs.” PLoS Computational Biology 14, no. 11 (November 29, 2018). https://doi.org/10.1371/journal.pcbi.1006626.
Campitelli, Paul, Jingjing Guo, Huan-Xiang Zhou, and S. Banu Ozkan. “A Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1.” The Journal of Physical Chemistry. B 122, no. 21 (May 31, 2018): 5623–29. https://doi.org/10.1021/acs.jpcb.7b11971.
Modi, Tushar, Jonathan Huihui, Kingshuk Ghosh, and S. Banu Ozkan. “Ancient Thioredoxins Evolved to Modern-Day Stability–Function Requirement by Altering Native State Ensemble.” Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1749 (June 19, 2018). https://doi.org/10.1098/rstb.2017.0184.
Modi, Tushar, and S. Banu Ozkan. “Mutations Utilize Dynamic Allostery to Confer Resistance in TEM-1 β-Lactamase.” International Journal of Molecular Sciences 19, no. 12 (November 29, 2018). https://doi.org/10.3390/ijms19123808.
2017
Larrimore, Katherine E., I. Can Kazan, Latha Kannan, R. Player Kendle, Tameem Jamal, Matthew Barcus, Ashini Bolia, et al. “Plant-Expressed Cocaine Hydrolase Variants of Butyrylcholinesterase Exhibit Altered Allosteric Effects of Cholinesterase Activity and Increased Inhibitor Sensitivity.” Scientific Reports 7 (September 5, 2017). https://doi.org/10.1038/s41598-017-10571-z.
2015
Butler, Brandon M., Z. Nevin Gerek, Sudhir Kumar, and S. Banu Ozkan. “Conformational Dynamics of Non-Synonymous Variants at Protein Interfaces Reveals Disease Association.” Proteins 83, no. 3 (March 2015): 428–35. https://doi.org/10.1002/prot.24748.
Kim, Hanseong, Taisong Zou, Chintan Modi, Katerina Dörner, Timothy J. Grunkemeyer, Liqing Chen, Raimund Fromme, Mikhail V. Matz, S. Banu Ozkan, and Rebekka M. Wachter. “A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins.” Structure (London, England : 1993) 23, no. 1 (January 6, 2015): 34–43. https://doi.org/10.1016/j.str.2014.11.011.
Kumar, Avishek, Brandon M. Butler, Sudhir Kumar, and S. Banu Ozkan. “Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine.” Current Opinion in Structural Biology 35 (December 2015): 135–42. https://doi.org/10.1016/j.sbi.2015.11.002.
Kumar, Avishek, Paul Campitelli, M. F. Thorpe, and S. Banu Ozkan. “Partial Unfolding and Refolding for Structure Refinement: A Unified Approach of Geometric Simulations and Molecular Dynamics.” Proteins83, no. 12 (December 2015): 2279–92. https://doi.org/10.1002/prot.24947.
Kumar, Avishek, Tyler J. Glembo, and S. Banu Ozkan. “The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin.” Biophysical Journal 109, no. 6 (September 15, 2015): 1273–81. https://doi.org/10.1016/j.bpj.2015.06.060.
2014
Bolia, Ashini, Z. Nevin Gerek, and S. Banu Ozkan. “BP-Dock: A Flexible Docking Scheme for Exploring Protein–Ligand Interactions Based on Unbound Structures.” Journal of Chemical Information and Modeling54, no. 3 (March 24, 2014): 913–25. https://doi.org/10.1021/ci4004927.
Bolia, Ashini, Brian W. Woodrum, Angelo Cereda, Melissa A. Ruben, Xu Wang, S. Banu Ozkan, and Giovanna Ghirlanda. “A Flexible Docking Scheme Efficiently Captures the Energetics of Glycan-Cyanovirin Binding.” Biophysical Journal 106, no. 5 (March 4, 2014): 1142–51. https://doi.org/10.1016/j.bpj.2014.01.040.
Mielke, Clinton, Natalie Lefort, Carrie G. McLean, Jeanine M. Cordova, Paul R. Langlais, Andrew J. Bordner, Jerez A. Te, S. Banu Ozkan, Wayne T. Willis, and Lawrence J. Mandarino. “Adenine Nucleotide Translocase Is Acetylated in Vivo in Human Muscle: Modeling Predicts a Decreased ADP Affinity and Altered Control of Oxidative Phosphorylation.” Biochemistry 53, no. 23 (June 17, 2014): 3817–29. https://doi.org/10.1021/bi401651e.
Zou, Taisong, Nickolas Williams, S. Banu Ozkan, and Kingshuk Ghosh. “Proteome Folding Kinetics Is Limited by Protein Halflife.” PLoS ONE 9, no. 11 (November 13, 2014). https://doi.org/10.1371/journal.pone.0112701.
2012
Glembo, Tyler J., Daniel W. Farrell, Z. Nevin Gerek, M. F. Thorpe, and S. Banu Ozkan. “Collective Dynamics Differentiates Functional Divergence in Protein Evolution.” PLoS Computational Biology 8, no. 3 (March 29, 2012). https://doi.org/10.1371/journal.pcbi.1002428.
2011
Gerek, Z. Nevin, and S. Banu Ozkan. “Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning.” PLoS Computational Biology 7, no. 10 (October 6, 2011). https://doi.org/10.1371/journal.pcbi.1002154.
2010
Gerek, Z Nevin, and S Banu Ozkan. “A Flexible Docking Scheme to Explore the Binding Selectivity of PDZ Domains.” Protein Science : A Publication of the Protein Society 19, no. 5 (May 2010): 914–28. https://doi.org/10.1002/pro.366.
Glembo, Tyler J., and S. Banu Ozkan. “Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction.” Biophysical Journal 98, no. 6 (March 17, 2010): 1046–54. https://doi.org/10.1016/j.bpj.2009.11.031.
2009
Shell, M. Scott, S. Banu Ozkan, Vincent Voelz, Guohong Albert Wu, and Ken A. Dill. “Blind Test of Physics-Based Prediction of Protein Structures.” Biophysical Journal 96, no. 3 (February 4, 2009): 917–24. https://doi.org/10.1016/j.bpj.2008.11.009.
2008
Dill, Ken A., S. Banu Ozkan, M. Scott Shell, and Thomas R. Weikl. “The Protein Folding Problem.” Annual Review of Biophysics 37 (June 9, 2008): 289–316. https://doi.org/10.1146/annurev.biophys.37.092707.153558.
2007
Ozkan, S. Banu, G. Albert Wu, John D. Chodera, and Ken A. Dill. “Protein Folding by Zipping and Assembly.” Proceedings of the National Academy of Sciences of the United States of America 104, no. 29 (July 17, 2007): 11987–92. https://doi.org/10.1073/pnas.0703700104.
2002
Ozkan, S. Banu, Ken A. Dill, and Ivet Bahar. “Fast-Folding Protein Kinetics, Hidden Intermediates, and the Sequential Stabilization Model.” Protein Science : A Publication of the Protein Society 11, no. 8 (August 2002): 1958–70.