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2025
E. Çiçek, Munar, İ., Çınar, S. Agopcan, Başçeken, S., Monard, G., Aviyente, V., and Sungur, F. Aylin, “Computational insights into substrate-assisted citrullination mechanisms of PAD2 isozyme: A comparative analysis of reaction pathways”, Journal of Molecular Graphics and Modelling, vol. 140, p. 109107, 2025.
Z. Ö. Güner-Yılmaz, Kocaaga, B., Yılmaz, A., Balcik, M., Kurkcuoglu, O., Sungur, F. Aylin, Yavuz, R., Karatepe, N., Tatlier, M., Sirkecioglu, A., Hooshmand, S., Miavaghi, M. Aliari, Zabara, M. Ahmed, Yürüm, A., Bayazıt, M. Kemal, Batirel, S., and F. Güner, S., “Graphene oxide-based and porous nanocarriers for drug delivery developed with computational and experimental approaches”, Surfaces and Interfaces, vol. 76, p. 107860, 2025.
Z. Sarica, Kurkcuoglu, O., and Sungur, F. Aylin, “In Silico Identification of Putative Allosteric Pockets and Inhibitors for the KRASG13D-SOS1 Complex in Cancer Therapy”, International Journal of Molecular Sciences, vol. 26, p. 3293, 2025.
2024
M. Yuce, Ates, B., Yasar, N. Isil, Sungur, F. Aylin, and Kurkcuoglu, O., “A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome”, Journal of Molecular Graphics and Modelling, vol. 131, p. 108817, 2024.
B. Kocaaga, Inan, T., Yasar, N. İsil, Yalcin, C. Ege, Sungur, F. Aylin, Kurkcuoglu, O., Demiroz, A., Komurcu, H., Kizilkilic, O., Aydin, S. Yekta, Ulgen, O. Aydin, Güner, F. Seniha, and Arslan, H., “Innovative Use of an Injectable, Self-Healing Drug-Loaded Pectin-Based Hydrogel for Micro- and Supermicro-Vascular Anastomoses”, Biomacromolecules, vol. 25, pp. 3959-3975, 2024.
2023
M. Tataroğlu and Sungur, F. Aylin, “Mechanistic insights into the challenges of organocatalytic Beckmann rearrangement reactions”, Org. Biomol. Chem., vol. 21, pp. 1254-1263, 2023.
2022
E. Cicek, Monard, G., and Sungur, F. Aylin, “Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations”, Biochemistry, vol. 61, pp. 1286-1297, 2022.
2021
M. Ayvaz Koroglu, Kurkcuoglu, O., and Sungur, F. Aylin, “Monte Carlo and Molecular Dynamics Simulations suggest controlled release of corticosteroids from mesoporous host MIL-101 (Cr)”, Molecular Simulation, vol. 47, pp. 1530–1539, 2021.
M. Yuce, Cicek, E., Inan, T., Dag, A. Basak, Kurkcuoglu, O., and Sungur, F. Aylin, “Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease”, Proteins: Structure, Function, and Bioinformatics, vol. 89, pp. 1425-1441, 2021.
2017
H. Kilic, Bayindir, S., Erdogan, E., S. Cinar, A., Konuklar, F. A. S., Bali, S. K., Saracoglu, N., and Aviyente, V., “Bismuth nitrate-promoted disproportionative condensation of indoles with cyclohexanone: a new-type azafulvenium reactivity of indole”, New J. Chem., vol. 41, pp. 9674-9687, 2017.
2015
H. H. Ince, F. Konuklar, A. Sungur, Ugur, I., Ö. Ozcan, A., Sayadi, M., Feig, M., and Aviyente, V., “Role of the n+1 amino acid residue on the deamidation of asparagine in pentapeptides”, Molecular Physics, vol. 113, pp. 3839–3848, 2015.
2014
E. Boz, Z. Haşlak, P., Tüzün, N. Ş., and F. Konuklar, A. Sungur, “A Theoretical Study On Rh(I) Catalyzed Enantioselective Conjugate Addition Reactions of Fluoroalkylated Olefins”, Organometallics, vol. 33, pp. 5111-5119, 2014.
2011
M. Çoban and F. Konuklar, A. S., “A computational study on the mechanism and the kinetics of urethane formation”, Computational and Theoretical Chemistry, vol. 963, pp. 168-175, 2011.
2009
C. Özen, F. Konuklar, A. S., and Tu̅zu̅n, N. S., “Mechanistic Study on [3+2] Cycloaddition and Cyclopropanation Reactions of 1,3-Dioxepine Derivatives in the Presence of Copper(I) Catalyst”, Organometallics, vol. 28, pp. 4964-4973, 2009.
2004
F. A. S. Konuklar, Aviyente, V., Monard, G., and Lopez, M. F. Ruiz, “Theoretical Approach to the Wear and Tear Mechanism in Triosephoshate Isomerase:  A QM/MM Study”, The Journal of Physical Chemistry B, vol. 108, pp. 3925-3934, 2004.
2001
A. (Sungur) F. Konuklar, Aviyente, V., Sen, T. Zafer, and Bahar, I., “Modeling the deamidation of asparagine residues via succinimide intermediates”, vol. 7, no. 5, pp. 147 - 160, 2001.

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