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Assoc. Prof. Dr. Abdulkadir KOÇAK
Chemistry

Abdulkadir KOÇAK
Phone
+90 (262) 6053083
Email
kocakgtu.edu.tr
Web page
http://www.modellab.org
Office
Chemistry, 138
Areas of interest
Molecular Spectroscopy Computational Chemistry Molecular modeling Free energy calculations Non-covalent interactions

27. S.G. Kankinou, M. Yildiz*, A. Kocak;"Exploring potential Plasmodium kinase inhibitors: a combined docking, MD and QSAR studies"; Journal of Biomolecular Structure and Dynamics, 2024, (in press)

26. U. Uzuner, E. Akkus, A. Kocak, S. Çelik Uzuner*; "Exploring epigenetic drugs as potential inhibitors of SARS-CoV-2 main protease: a docking and MD simulation study;"Journal of Biomolecular Structure and Dynamics, 2024, (in press)

25. H.S. Tasci, E. Akkus, M. Yildiz*, A. Kocak; "Computational analysis of substrate recognition of Sars-Cov-2 Mpro main protease"; Computational Biology and Chemistry, 2023, 107, 107960

24. E. Akkus, O. Tayfuroglu, M. Yildiz, A. Kocak*; "Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant"; Journal of Physical Chemistry B, 2023, 127, 20, 4415–4429

23. M. Temel, O. Tayfuroglu, A. Kocak*; "The performance of ANI‐ML potentials for ligand‐n(H2O) interaction energies and estimation of hydration free energies from end‐point MD simulations" Journal of Computational Chemistry, 2023, 44 (4), 559-569

22. E. Akkus, O. Tayfuroglu, M. Yildiz, A. Kocak*;"Accurate Binding Free Energy Method from End-State MD Simulations"Journal of Chemical Information and Modeling, 2022, 62 (17), 4095-4106

21. A. Kocak*, M Yildiz "Molecular dynamics simulations reveal the plausible agonism/antagonism mechanism by steroids on androgen receptor mutations"; Journal of Molecular Graphics and Modelling, 2022, 111, 108081

20. O. Tayfuroglu, A. Kocak, Y. Zorlu*; "A neural network potential for the IRMOF series and its application for thermal and mechanical behaviors";Physical Chemistry Chemical Physics, 2022, 24 (19), 11882-11897

19. E. Bağda, E. Bağda, A. Kocak, M. Durmuş* "Investigation of Binding behaviour of a water-soluble gallium (III) phthalocyanine with double-stranded and G-quadruplex DNA via experimental and computational methods";Journal of Molecular Structure, 2021, 1240, 130536

18. S.Y. Al-Raqa, K. Khezami, E.N. Kaya, A. Kocak, M. Durmuş*, "Experimental and theoretical investigation of water-soluble silicon (IV) phthalocyanine and its interaction with bovine serum albumin"; JBIC Journal of Biological Inorganic Chemistry, 2021, 26, 235-247

17. O. Tayfuroglu, A. Kocak* and Y. Zorlu;"In silico investigation into H2 uptake in MOFs: combined text/data mining and structural calculations"; Langmuir, 2019,36 (1), 119-129

16. A. Kocak*; "HBGA binding modes and selectivity in noroviruses upon mutation: A docking and molecular dynamics study;Journal of Molecular Modeling, 2019, 25, 369

15. M. Yildiz* and A. Kocak;"Computational Interrogation of the human norovirus-host cell interactions faciliated by A-type antigen";Sakarya University Journal of Science, 2019, 23,1056-1065

14. A. Kocak* and M. Yildiz;"Molecular dynamics studies of the norovirus-host cell interaction mediated by H-type1 antigen";Trakya University Journal of Natural Sciences, 2019, 20,19-26

13. M. Yildiz* and A. Kocak;"Molecular dynamics of HBGA blocking human IgA antibody and escape mechanism in noroviruses";Journal of Computational Biology, 2019, 26, 964-972

12. H. Kandemir, A. Kocak, S. O. Tumay, B. Cosut, Y. Zorlu and I. F. Sengul*;"Experimental and theoretical studies of carbazole-based Schiff base as a fluorescent Fe+ probe";Journal of Turkish Chemistry, 2018, 42, 221-236

11. H. Yilmaz*, A. Kocak, M. Dilimulati, Y. Zorlu and M. Andac;"A new Co(III) complex of Schiff base derivative for electrochemical recognition of nitrite anion";Journal of Chemical Sciences, 2017, 129, 1559-1569

10. A. Kocak* and M. Yildiz ;"Docking, molecular dynamics and free energy studies on aspartoacylase mutations involven in Canavan disease",Journal of Molecular Graphics and Modelling, 2017, 74, 44-53

9. A. Kocak*, I. Erol, M. Yildiz and H.Can;"Computational insights into the protonation states of catalytic dyad in BACE1-acyl guanidine based inhibitor complex"; Journal of Molecular Graphics and Modelling, 2016, 70, 226-235.

8. A. Kocak*, H. Yilmaz, O. Faiz and O. Andac;"Experimental and theoretical studies on Cu(II) complex of N,N'-disalicylidene-2,3-diaminopyrıdıne ligand reveals indirect evidence for DNA intercalation"; Polyhedron, 2016, 104, 106-115.

7. M. A. Ashraf, C. W. Copeland, A. Kocak, A. R. McEnroe and R. B. Metz*;"Vibrational spectroscopy and theory of Fe2+(CH4)n (n=1-3)"; Physical Chemistry Chemical Physics, 2015, 17, 25700-25704.

6. A. Kocak, M. A. Ashraf and R. B. Metz*;"Vibrational spectroscopy reveals varying structural motifs in Cu+(CH4)n and Ag+(CH4)n (n=1-6)"; Journal of Physical Chemistry A, 2015, 119, 9653-9665.

5. W. L. Pearson, III, C. Copeland, A. Kocak, Z. Sallese and R. B. Metz*;"Near ultraviolet photodissociation spectroscopy of Mn+(H2O) and Mn+(D2O)"; Journal of Chemical Physics, 2014, 141.

4. A. Kocak, Z. Sallese, M. D. Johnston and R. B. Metz*;"Vibrational spectroscopy of Co+(CH4)n and Ni+(CH4)n (n=1-4)"; Journal of Physical Chemistry A, 2014, 118, 3253-3265.

3. A. Kocak, G. Austein-Miller, W. L. Pearson, III, G. Altinay and R. B.
Metz*; "Dissociation energy and Electronic and vibrational spectroscopy of Co+(H2O) and its isotopomers"; Journal of Physical Chemistry A, 2013, 117, 1254-1264.

2. J. S. Daluz, A. Kocak and R. B. Metz*; "Photodissociation studies of the electronic and vibrational spectroscopy of Ni+(H2O)"; Journal of Physical Chemistry A, 2012, 116, 1344-1352.

1. G. Altinay, A. Kocak, J. S. Daluz and R. B. Metz*; "Electronic and vibrational spectroscopy of intermediates in methane-to-methanol conversion by CoO+"; Journal of Chemical Physics, 2011, 135.

  • Third Cycle (Doctoral): 2010-2014 University of Massachusetts-Amherst
  • Second Cycle (Master's): 2008-2010 University of Massachusetts-Amherst
    2005-2007 Ondokuz Mayıs Üniversitesi*
  • First Cycle (Undergraduate): 2001-2004 Ondokuz Mayıs Üniversitesi
    2000-2001 Kahramanmaras Sütçü İmam Üniversitesi*
2007-2008 Syracuse University, English Language Institute, (Non-degree)
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