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Current Research Activities:

We identify molecular interactions and trace their communication pathways on different time and length scales. We ferret out the relationships between local motifs and global patterns in complex networks with arbitrary degree distributions. These activities find technological applications in devising molecular machines and system identification tools.  For more information about my research, click here.

Selected Recent Publications  

• M. S. Manna, Y. T. Tamer, I. Gaszek, N. Poulides, A. Ahmed, X. Wang, F. C. R. Toprak, D. R. Woodard, A. Y. Koh, N. S. Williams, D. Borek, A. R. Atilgan, J. D. Hulleman, C. Atilgan, U. Tambar, and E. Toprak, “A trimethoprim derivative impedes antibiotic resistance evolution,” Nature Communications, Vol. 12, 2021, 2249/1-10. [LINK]
• Guclu, T. F., A. R. Atilgan, and C. Atilgan, “Dynamic Community Composition Unravels Allosteric Communication in PDZ,” The Journal of Physical Chemistry B, Vol. 125 (9), 2021, pp. 2266 – 2276. [LINK]
• Guclu, T. F., N. Kocatug, A. R. Atilgan, and C. Atilgan, “N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding ,” Journal of Chemical Information and Modeling, Vol. 61 (1), 2021, pp. 347 – 357. [LINK]
• Abdizadeh, H., F. Jalalypour, A. R. Atilgan, and C. Atilgan, “A coarse-grained methodolody identifies intrinsic mechanisms that dissociate interacting protein pairs,” Frontiers in Molecular Biosciences, Vol. 7, 210, 2020, pp. 1 – 18. [LINK]
• Tamer, Y. T., I. K. Gaszek, H. Abdizadeh, T. Bature, K. Reynolds, A. R. Atilgan, C. Atilgan, and E. Toprak, “High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection,” Molecular Biology and Evolution, Vol. 36 (7), 2019, pp. 1533 – 1550. [LINK]
• Ross, C. J., B. Nizami, M. Glenister, O. S. Amamuddy, A. R. Atilgan, C. Atilgan, and O. T. Bishop, “MODE-TASK: Large-scale Protein Motion Tools,” Bioinformatics, Vol. 34 (21), 2018, pp. 3759 – 3763. [LINK] 
• Ross, C. J., A. R. Atilgan, O. T. Bishop, and C. Atilgan, “Unraveling the Motions behind Enterovirus 71 Uncoating,” Biophysical Journal, Vol. 114(4), 2018, pp. 822 – 838. [LINK] Also find a [movie] visualizing first non-degenerate mode of pentamer complex, which is the minimal functional unit explaining virus deformations.
• Ozbaykal, G., A. R. Atilgan, and C. Atilgan, “In Silico Mutational Studies of Hsp70 Disclose Sites with Distinct Functional Attributes,” Proteins: Structure, Function, Bioinformatics, Vol. 83, No. 11 [Cover Image] 2015, pp. 2077 – 2090. [LINK]
• Atilgan, C., O. B. Okan, and A. R. Atilgan, “Network-based Models as Tools Hinting at Non-evident Protein Functionality,” Annual Review of Biophysics, Vol. 41, 2012, pp. 205 – 225. [LINK]