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
degree distributions. These activities find technological applications
molecular machines and system identification tools.
[Researcher ID: A-7805-2011]
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]
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]
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.
G., A. R. Atilgan, and C. Atilgan, "In Silico Mutational Studies of
Hsp70 Disclose Sites with Distinct Functional Attributes," Proteins:
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]
Graduating Class Award, selected by the
senior students of the Sabanci University, 2012 (first place), 2016 (second place), 2017 (first place). [LINK]
Outstanding Achievement in Education
Prize, awarded by the Bogazici
Outstanding Achievement in Research Prize, awarded by the Bogazici
Young Scientist Encouragement Prize (nationwide), given by the
Scientific and Technical Research Council of Turkey, 1995.
Jefferson Goblet Paper Award (nationwide, first place) given by the
American Institute of Aeronautics and Astronautics, 1989.
"Empirically Tractable Antibiotics Time Machines," [VI. Ecology and Evolutionary Biology Symposium], Ankara University, 10-12 July 2019.
"Overhauling A Popular Introductory Engineering Course: ENS 208," [The Second Education Conference], Sabanci University, 28-29 May 2019 [Abstracts].
"Morphogenesis a la Schelling," [Queen Mary University of London], 24 January 2019.
"Unraveling the Motions behind Enterovirus 71 Uncoating," 17th European Conference on Computational Biology, Highlights - Proteins, Athens, 8-12 September 2018 [Programme].
"Biological physics of enterovirus coarsening," 4th International Scientific and the 5th MC meeting of the COST Action CM1306 'Understanding Movement and Mechanisms in Molecular Machines,' Zagreb, 21-24 March 2018 [Programme].
"The spread of influence through a network society," ESRC Business and Local Government, [BLG Data Research] Center, 31 January 2018, [Webinar].
"To be a part of a network or not to be," [University of Essex], 24 January 2018.
"Maze generators and collective action in networks," [McCormick-Civil and Environmental Engineering], Northwestern University, 10 November 2017.
"Collective action in social networks," [24th Statistical Physics Days], [Izmir Institute of Technology], 29 June - 2 July 2017.