Our Publications
Note
An ‘IF10+‘ label is appended to citations for articles published in journals with an impact factor greater than 10. The designation ‘Lead‘ is added to publications where Dr. Gur served as any of the following: first author, co-first author, corresponding author, or co-corresponding author. Journal Impact Factors (IF) are based on the 2023 release of Journal Citation Reports unless otherwise indicated, with the format (5-year IF, 2023 IF).
Dr. Mert Gur held a lead role in 28 out of 39 journal articles.
Journal Articles
39. Rashidi, H.H., Pantanowitz, J., Hanna, M., Tafti, A.P., Sanghani, P., Buchinsky, A., Fennell, B., Deebajah, M., Wheeler, S., Pearce, T., Abukhiran, I., Robertson, S., Palmer, O., Gur, M., Tran, N.K., Pantanowitz, L. (2025) Introduction to AI-ML in Pathology & Medicine: Generative & Non-Generative AI Basics, Modern Pathology, 100688 (5-year IF: 6.8, IF: 7.1)
38. Yang-Schulz, A., Zacharopoulou, M., Yilmaz, S.Z., Banerjee, A., Saha, S., Nietlispach, D., Ohlmeyer, M., Gur, M., Itzhaki, L.S., Bahar, I., Gordon, R. (2025) Observing real-time binding of a small molecule activator of protein phosphatase 2A at the single molecule level, npj Biosensing, 2(1): 2.
37. Rashidi, H.H., Hu, B., Pantanowitz, J., Tran, N., Liu, S., Chamanzar, A., Gur, M., Tafti, A., Pantanowitz, L., Hanna, M. (2024) Statistics of Generative AI & Non-Generative Machine Learning Studies in Medicine, Modern Pathology, (Accepted) (5-year IF: 6.8, IF: 7.1)
36. Zhang, H., Gur, M., Bahar, I. (2024) Global hinge sites of proteins as target sites for drug binding, PNAS, 121 (49): e2414333121 (IF10+, 5-year IF: 10.8, IF: 9.4)
35. Gur, M., Golcuk, M., Bahar, I. (2024) Elastic Network Models in protein dynamics: Bridging simplicity and complexity, AsiaChem, 4(1):158-165 (Lead, Corresponding Author)
34. Salvador-Garcia, D., Jin, L., Hensley, A., Golcuk, M., Gallaud, E., Chaaban, S., Port, F., Vagnoni, A., Planelles-Herrero, V.J., McClintock, M.A., Derivery, E., Carter, A.P., Giet, R., Gur, M., Yildiz, A., Bullock, S.L. (2024). A force-sensitive mutation reveals a non-canonical role for dynein in anaphase progression, Journal of Cell Biology, 223 (10): e202310022 (5-year IF: 8, IF: 7.3)
33. Banerjee, A., Mathew, S., Naqvi, M. M., Yilmaz, S. Z., Zacharopoulou, M., Doruker, P., Kumita, J. R., Yang, S., Gur, M., Itzhaki, L. S., Gordon, R., Bahar, I. (2024) Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezer, Science Advances, 10, eadn2208 (Lead, Corresponding author) (IF10+,5-year IF: 13.8, IF:11.7)
32. Golcuk, M., Yilmaz, S. Z., Yildiz, A., Gur, M. (2024). The Mechanism and energetics of the dynein priming stroke, Structure, 32(5):603-610.e604 (Lead, Corresponding author) (5-year IF: 4.3, IF: 4.4)
31. Costa, M. G. S., Gur, M., Krieger, J. M., Bahar, I. (2024). Computational biophysics meets cryo-EM revolution in the search for the functional dynamics of biomolecular systems, WIREs Computational Molecular Science, 14(1):e1689 (Lead, Co-first author) (IF10+,5-year IF: 20, IF: 16.8)
30. Golcuk M., Yildiz, A., Gur, M. (2022). Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2. Journal of Molecular Graphics and Modelling, 117, 108286 (Lead, Corresponding author) (5-year IF: 2.4, IF: 2.7)
29. Golcuk M., Hacisuleyman, A., Yilmaz, S. Z., Taka, E. Yildiz A., Gur. M. (2022). SARS-Cov-2 delta variant decreases nanobody binding and ACE2 blocking effectivity. Journal of Chemical Information and Modeling, 62 (10), 2490-2498. (Lead, Corresponding author) (5-year IF: 5.9, IF: 5.7)
28. Ferro, L. S., Fang, Q., Eshun-Wilson, L., Fernandes, J., Jack, A., Farrell, D. P., Golcuk, M., Huijben, T., Costa, K., Gur, M., DiMaio, F., Nogales, E., Yildiz, A., (2022) Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7. Science, 375(6578), 326-331. (IF10+, 5-year IF: 50.3, IF: 44.8)
27. Gur, M., Yilmaz, S. Z., Taka, E. (2021). The first law of thermodynamics analysis of transporters involved in the glutamate/gaba-glutamine cycle. Journal of Thermal Science and Technology, 41(2), 265-276. (Lead, First and corresponding author)
26. Golcuk, M., Hacisuleyman, A., Erman, B., Yildiz, A., Gur M. (2021). Binding mechanism of neutralizing nanobodies targeting SARS-CoV-2 spike glycoprotein. Journal of Chemical Information and Modeling, 61(10), 5152–5160. (Lead, Corresponding author) (5-year IF: 5.9, IF: 5.7)
25. Taka, E., Yilmaz, S. Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2021). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor. The Journal of Physical Chemistry B, 125 (21), 5537-5548. (Lead, Corresponding author) (5-year IF: 2.8, IF: 2.8)
24. Ferro, L., Eshun-Wilson, L., Golcuk, M., Fernandes, J., Huijben, T., Gerber, E., Jack, A., Costa, K., Gur, M., Fang, Q., Nogales, E. and Yildiz, A. (2020). The mechanism of motor inhibition by microtubule-associated proteins. bioRxiv (Preprint)
23. Gur, M., Taka, E., Yilmaz, S. Z., Kilinc, C., Aktas, U., Golcuk, M. (2020). Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states. The Journal of Chemical Physics, 153(7), 075101 (Lead, First and corresponding author) (5-year IF: 3.6, IF: 3.1)
22. Gur, M. (2020). COVID-19 Aşı ve ilaç geliştirme çalışmalarında spike glikoproteininin yeri ve önemi (The role and importance of spike glycoprotein in COVID-19 vaccine and drug development studies). Turkish Academy of Sciences (TÜBA) Günce, 63, 57-60 (Lead, First and corresponding author)
21. Gur, M., Golcuk, M., Gul, A., Erman, B. (2020). Molecular dynamics simulations provide molecular insights into the role of HLA-B51 in Behçet’s disease pathogenesis. Chemical Biology & Drug Design, 96(1), 644-658 (Lead, Corresponding author) (5-year IF: 2.9, IF: 3.2)
20. Zhou, Z., Feng, Z., Hu, D., Yang, P., Gur, M., Bahar, I., Cristofanilli, M., Gradishar, W.J., Xie, X., Wan, Y. (2019). A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for target therapy. EBioMedicine- The Lancet, 44, 98-111 (5-year IF: 9.2, IF: 9.7)
19. Gur, M., Golcuk, M., Yilmaz, S. Z., Taka, E. (2019). Thermodynamic first law efficiency of membrane proteins. Journal of Biomolecular Structure and Dynamics, 38(2), 439–449 (Lead, First and corresponding author) (5-year IF: 3.2, IF: 2.7)
18. Can, S., Lacey, S., Gur, M., Carter, A. P., Yildiz, A. (2019). Directionality of dynein is controlled by the angle and length of its stalk. Nature, 566(7744), 407-410 (IF10+, 5-year IF: 54.4, IF:50.5)
17. Pullara, F., Wenzhi, M., Gur, M. (2019). Why protein conformers in molecular dynamics simulations differ from their crystal structures: a thermodynamic insight. Turkish Journal of Chemistry, 43(2), 394-403 (Lead, Corresponding author) (5-year IF: 1.2, IF: 1.3)
16. Gur, M., Blackburn, E. A., Ning, J., Narayan, V., Ball, K. L., Walkinshaw, M. D., Erman, B. (2018). Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties. The Journal of Chemical Physics, 148(14), 145101 (Lead, First and co-corresponding author) (5-year IF: 3.6, IF: 3.1)
15. Gur, M., Cheng, M. H., Zomot, E., Bahar, I. (2017). Effect of dimerization on the dynamics of neurotransmitter: sodium symporters. The Journal of Physical Chemistry B, 121(15), 3657-3666 (Lead, First and co-corresponding author) (5-year IF: 2.8, IF: 2.8)
14. Gur, M. (2016). Experimental and theoretical investigation of pumpkin drying in fluidized bed dryer. Uludağ University Journal of The Faculty of Engineering, 21(2), 145-158 (Lead, First and corresponding author)
13. Gur, M., Zomot, E., Cheng, M. H., Bahar, I. (2015). Energy landscape of LeuT from molecular simulations. The Journal of Chemical Physics, 143 (24), 243134 (Lead, First author) (5-year IF: 3.6, IF: 3.1)
12. Hu, D.*, Gur, M.*, Zhou, Z., Gamper, A., Hung, M. C., Fujita, N., Lan L, Bahar I., Wan, Y. (2015). Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. Nature Communications, 6(1), 8419 (Lead, Co-First author) (IF10+, 5-year IF: 14.7, IF: 16.1)
11. Zomot, E., Gur, M., Bahar, I. (2015). Microseconds simulations reveal a new sodium-binding site and the mechanism of sodium-coupled substrate uptake by LeuT. Journal of Biological Chemistry, 290(1), 544-555 (5-year IF: 4.4, IF: 4)
10. Das, A., Gur, M., Cheng, M. H., Jo, S., Bahar, I., Roux, B. (2014). Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLOS Computational Biology, 10(4), e1003521 (Lead, Co-first author) (5-year IF: 4.3, IF: 3.8)
9. Gur, M., Madura, J. D., Bahar, I. (2013). Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophysical Journal, 105(7), 1643-1652 (Featured as new and notable) (Lead, First author) (5-year IF: 3.2, IF: 3.2)
8. Gur, M., Zomot, E., Bahar, I. (2013). Global motions exhibited by proteins in micro-to milliseconds simulations concur with anisotropic network model predictions. The Journal of Chemical Physics, 139(12), 121912 (Lead, First author) (5-year IF: 3.6, IF: 3.1)
7. Eskici, G., Gur, M. (2013). Computational design of new peptide inhibitors for amyloid beta (Aβ) aggregation in Alzheimer’s disease: application of a novel methodology. PLOS One, 8(6), e66178 (Lead, Corresponding author) (5-year IF: 3.3, IF: 2.9)
6. Gur, M., Erman, B. (2012). Quasi‐harmonic fluctuations of two bound peptides. Proteins: Structure, Function, and Bioinformatics, 80(12), 2769-2779 (Lead, First and corresponding author) (5-year IF: 2.8, IF: 3.2)
5. Arkun, Y., Gur, M. (2012). Combining optimal control theory and molecular dynamics for protein folding. PLOS One, 7(1), e29628 (5-year IF: 3.3, IF: 2.9)
4. Meireles, L., Gur, M.*, Bakan, A.*, Bahar, I.* (2011). Pre‐existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Science, 20(10), 1645-1658 (Lead, Co-First author) (5-year IF: 9.1, IF: 4.5)
3. Kabakçioğlu, A., Yuret, D., Gur, M., Erman, B. (2010). Anharmonicity, mode-coupling and entropy in a fluctuating native protein. Physical Biology, 7(4), 046005. (5-year IF: 1.7, IF: 2)
2. Gur, M., Erman, B. (2010). Quasi-harmonic analysis of mode coupling in fluctuating native proteins. Physical Biology, 7(4), 046006 (Lead, First author) (5-year IF: 1.7, IF: 2)
1. Yogurtcu, O. N., Gur, M., Erman, B. (2009). Statistical thermodynamics of residue fluctuations in native proteins. The Journal of Chemical Physics, 130(9), 03B607 (5-year IF: 3.6, IF: 3.1)
Book Chapters
2. Gur, M. (2020) Exploring conformational transition of 2019 novel coronavirus spike glycoprotein between its closed and open states using molecular dynamics simulations. In M., Şeker, A., Özer, Z., Tosun, C., Korkut, M., Doğrul (Ed.). TÜBA Assessment Report on COVID-19 Global Outbreak (pp. 161). Ankara, Turkey: Turkish Academy of Sciences Publications
1. Gur, M., Gur, M. (2014). Comparing corn drying in fluidized bed dryer and convective tray dryer. In I., Dincer, A., Midilli, H., Kucuk (Ed.). Progress in Exergy Energy and the Environment (pp. 1085). Springer International Publishing.(Corresponding author)
Conferences, Symposia and Meetings
39. Golcuk, M., Yilmaz, S. Z., Yildiz, A., Gur, M (2023). Exploring the Priming Stroke of Dynein-2 Linker Through Microseconds-Long Molecular Dynamics Simulations. 9th International BAU Drug Design Congress. Istanbul, Turkey
38. Gur, M. (2023). Computational Odyssey: Molecular Marvels in Structural Biology. Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS). Phoenix, AZ
37. Golcuk, M., Yilmaz, S. Z., Yildiz A. Gur M. (2022) The mechanism and energetics of the dynein priming stroke. 8th International BAU-Drug Design Congress. Istanbul, Turkey
36. Buran C. H., Taka, E., Gur M. (2022) Investigation of the structural differences between wild-type and mutant forms of mutsa Heterodimer with Molecular Dynamic Simulations. 8th International BAU-Drug Design Congress. Istanbul, Turkey
35. Yilmaz, S. Z., Golcuk, M., Erman, B., Gur, M. (2022). Modelling cell membrane passing mechanism and energetics of cell penetrating peptides comprising HLA-B*51 binding motifs. International Congress of the Molecular Biology Association of Turkey (MolBiyoKon22). Istanbul, Turkey
34. Dingiloglu, B., Basturk, E., Turk M., Golcuk M., Eyupoglu, A. E., Karakus, B. Z., Can O., Erman B., Gur M., Dinler-Doğanay, G. (2022). Developing novel peptide-based inhibitor candidates against receptor binding domain (RBD) of SARS-CoV-2 spike protein. International Congress of the Molecular Biology Association of Turkey (MolBiyoKon22). Istanbul, Turkey
33. Gur, M. (2021). Exploring conformational transitions during the CHK2 activation via Molecular Dynamics Simulations. 3rd International Cancer and Ion Channels Congress (CANCERION-2021). (Invited Speaker)
32. Gur, M., Yilmaz, S.Z., Taka, E. (2021). Thermodynamic first law analysis of transporters involved in the Glutamate/GABA-Glutamine cycle. 23rd Congress on Thermal Science and Technology.
31. Golcuk M., Hacisuleyman A., Erman B., Yildiz A., Gur M. (2021). Exploring the binding mechanisms of nanobodies targeting SARS-CoV-2 spike glycoprotein using Molecular Dynamics Simulations. 2021 ACS Fall Meeting. (Atlanta, GA) (Invited Speaker)
30. Taka, E., Yilmaz, S.Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2021). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor. 2021 ACS Spring Meeting. (Invited Speaker)
29. Gur, M. (2021). Molecular Dynamics Simulations of large biomolecular systems. High Performance Computing Technologies in Drug Design Workshop. (Invited Speaker)
28. Taka, E., Yilmaz, S.Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2021). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor. ITU Department of Chemical Engineering 2nd Graduate Symposium. (Invited Speaker) Istanbul, Turkey
27. Gur, M., Can, S., Lacey, S., Carter, A. P., Yıldız, A. (2019). Modelling plus-end-directed dyneins. 7th International Congress of the Molecular Biology Association of Turkey (MolBiyoKon19). Istanbul, Turkey
26. Gur, M., Golcuk, M., Gul, A., Erman, B. (2019). Molecular overview of the role of HLA-B51 in Behçet’s disease. 7th International Congress of the Molecular Biology Association of Turkey (MolBiyoKon19). Istanbul, Turkey
25. Gur, M. (2019). Insight into the mechanochemical cycle of cytoplasmic dynein from molecular dynamics simulations. 7th International BAU Drug Design Congress. (Invited Speaker) Istanbul, Turkey
24. Golcuk, M., Taka, E., Yilmaz, S.Z., Gur, M. (2019). Molecular Dynamics Simulations of the dynein linker movement. The 12th International Symposium on Health Informatics and Bioinformatics. Izmır, Turkey
23 Can, S., Lacey, S., Gur, M., Carter, A. P., Yildiz, A. (2019). Dynein’s directionality is controlled by the angle and length of its stalk. 63rd Annual Meeting of the Biophysical-Society. Baltimore, MD
22. Gur, M., Can, S., Lacey, S., Carter, A. P., Yildiz, A. (2018). Engineering plus-end directed dyneins. 6th International BAU Drug Design Congress. Istanbul, Turkey
21. Gur, M., Gul, A., Erman, B. (2018) Dynamic and static differences between conformations of HLA-B51 and HLA-B52: implications for the pathogenic mechanisms of HLA-B51 in Behçet’s disease. 6th International BAU Drug Design Congress. Istanbul, Turkey
20. Gur, M., Golcuk, M., Yilmaz, S. Z., Taka, E. (2018). Thermodynamic first law analysis of proteins. 6th International BAU Drug Design Congress. Istanbul, Turkey
19. Gur, M., Cheng, M. H., Zomot, E.,Bahar, I. (2017). Importance of dimerization in facilitating the functional dynamics of neurotransmitter: Sodium symporters. 61st Annual Meeting of the Biophysical-Society.New Orleans, LA
18. Gur, M., Cheng, M. H., Zomot, E., Bahar, I. (2017). Investigation of the effect of dimerization on the functional dynamics of neurotransmitter: Sodium symporters. 5th International BAU-Drug Design Congress. Istanbul, Turkey
17. Gur, M., Zomot, E., Cheng, M. H., Bahar, I. (2015). Insight into the dynamics of LeuT from multiscale simulations. Gordon Research Conferences (GRC) Mechanism of Membrane Transport. Lewiston, ME.
16. Gur, M., Zomot, E., Cheng, M. H., Bahar I. (2014). Toward gaining a mechanistic understanding of substrate transport by LeuT. Gordon research Conferences (GRC) Biopolymers. Newport, RI.
15. Gur, M., Zomot, E., Bahar, I. (2014). Global motions of proteins observed in micro to milliseconds simulations concur with Anisotropic Network Model predictions. Membrane Protein Structural Dynamics Consortium’s Annual Meeting. Chicago, IL
14. Das, A., Gur, M., Bahar, I., Roux, B. (2013). A simple coarse-grained model to map the transition pathway between two stable conformations using the Anisotropic Elastic Network model. 57th Annual Meeting of the Biophysical-Society. Philadelphia, PA
13. Gur, M., Eskici, G. (2013). Computational design of new peptide inhibitors for amyloid beta aggregation in Alzheimer’s disease application of a novel methodology. American Institute of Chemical Engineers (AIChE) Annual Meeting. San Francisco, CA.
12. Gur, M., Zomot, E., Bahar, I. (2013). Multiscale investigation of biomolecular systems dynamics. American Institute of Chemical Engineers (AIChE) Annual Meeting. San Francisco, CA.
11. Gur, M., Gur, M. (2013). Comparing corn drying in fluidized bed dryer and convective tray dryer. The Sixth International Exergy, Energy and Environment Symposium. Rize, Turkey
10. Gur, M., Madura, J., Bahar, I. (2013). Global transitions or proteins explored by a multiscale hybrid methodology: Application to dopamine transporter. 57th Annual Meeting of the Biophysical-Society. Philadelphia, PA
9. Gur, M., Madura, J., Bahar, I. (2012). Transition pathways of Dopamine transporters explored by combining Molecular Dynamics simulations and Monte Carlo sampling of collective modes. Membrane Protein Structural Dynamics Consortium’s Annual Meeting. Chicago, IL.
8. Gur, M., Madura, J., Bahar, I. (2012). Transition pathways of proteins explored by combining Molecular Dynamics simulations and Monte Carlo sampling of collective modes. Biophysical Society 56th Annual Meeting. Philadelphia, PA.
7. Arkun, Z.Y., Gur, M. (2011). Protein folding using coarse grained optimal control and Molecular Dynamics. 18th International Federation of Automatic Control (IFAC) World Congress. Milano, Italy.
6. Gur, M., Bahar, I. (2011). Transition pathways of enzymes explored by combining the Anisotropic Network Model, Molecular Dynamics Simulations and a Monte Carlo sampling of conformational space. Albany 2011: Conversation 17. Albany, NY.
5. Gur, M., Erman, B. (2010). Harmonic fluctuations of two bound peptides. Gordon Research Conference (GRC) Biopolymers. Newport, RI.
4. Gur, M., Erman, B. (2010). Coupling between energy and residue position fluctuations in native proteins. 5th International Symposium on Health Informatics and Bioinformatics. Antalya, Turkey
3. Gur, M., Erman, B. (2009). Statistical thermodynamics and mode analysis of residue fluctuations in native proteins. Gordon Research Conference (GRC) Computer Aided Drug Design. Tilton, NH.
2. Gur, M., Erman, B. (2009). Statistical thermodynamics of residue fluctuations in native proteins. Biophysical Society 53rd Annual Meeting. Boston, MS.
1. Gur, M., Erman, B. (2008). Determining binding forces between two peptides using the Gaussian Network Model. XXI Sitges Conference-Statistical Mechanics of Biopyhsics. Sitges, Spain