Türkçe MyKHAS

mbg-Publications

2023

    • Sireci, S., Kocagöz, Y., Alkiraz, A. S., Güler, K., Dokuzluoglu, Z., Balcioglu, E., Meydanli, S., Demirler, M. C., Erdoğan, N. M., & Fuss, S. H. (2023). HB‐EGF promotes progenitor cell proliferation and sensory neuron regeneration in the zebrafish olfactory epithelium. The FEBS Journal.

         DOI:https://doi.org/10.1111/febs.17033

    • Büşra Osma, Önder Pekcan, Gülşen Akın Evingür “ Kinetic Models For PAAm-GO Composites As Antifoulant “Polymer Engineering and Science (2023) ; 63:238–248.
    • Ünver, G. Evingür and Ö Pekcan” Optical and Mechanical PROPERTIES OF PNIPAm-MWCNTs and PNIPAm-GO COMPOSITES “ Journal of Applied Polymer Science 140,9, e53539( 2023).
    • Arsan, Ö. Pekcan “Chaotic-Deterministic and/or Random Nature of Earth Quakes; A Phase Space Analysis“.Symmetry: Culture and Science Pg 45-59, Vol. 34, No.1, (2023) .
    • Arda, S. Kara, F. Dolaştır and Ö. Pekcan, G. Evingür” A QCM Study on Formation Of Aquaous K-Carrageenan-Chitosan Composite Bilayers with NaCl And GO” J. Macromolecular Sci. Phys. B, online: 02 Jun 2023.
    • Selcuk Ogrenci, Metehan Incegul, Onder Pekcan, A. Humeyra Bilge “Epidemic Models for Chemical Gel Phase Transformation: Effect of Optical Measurements with Different Wavelengths” J. macromol Sci.Phys. B 62,2, 2023/4/17.

    • Zeynep Kalaycıoğlu, Bengü Özuğur Uysal, Önder Pekcan, F. Bedia Erim*” Efficient photocatalytic degradation of methylene blue dye from aqueous solution with cerium oxide nanoparticles and graphene oxide doped polyacrylamide” ACS Omega 2023/3/29.

    • Baykaş, F. Kaan, A. F. Gürsoy M. Hekimoğlu and Ö. Pekcan “Residual LSTM Neural Network for Time Dependent Consecutiv Pitch  String Recognition from Spectrograms: A Study on Turkish Classical Music Makams”, (in press) Multimedia Tools and Applications.

    • Sarah Boumezber; Kemal Yelekci, “Synthesizing of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques”, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2023) 41 (8) p.3607-3629, DOI:10.1080/07391102.2022.2054471

    • Ecem Gokoglan; Damla Dere; Ipek Bedir; Kemal Yelekci; Dilek Telci; S. Guniz Kucukguzel; K., “Synthesis and investigation of cytotoxic effects of compounds derived from flurbiprofen”, JOURNAL OF MOLECULAR STRUCTURE (2023) 1289, DOI: 10.1016/j.molstruc.2023.135876

    • Gizem Erensoy; Kai Ding; Chang-Guo Zhan; Gamze Ciftci; Kemal Yelekci; Merve Duracik; Ozlem Bingol Ozakpinar; Esra Aydemir; Zubeyde Nur Yilmaz; Fikrettin Sahin; Necla Kulabas; Esra Tatar; Ilkay Kucukguzel., “Synthesis, in vitro and in silico studies on novel 3-aryloxymethyl-5-[(2-oxo-2-arylethyl)sulfanyl]-1,2,4-triazoles and their oxime derivatives as potent inhibitors of mPGES-1”, JOURNAL OF MOLECULAR STRUCTURE (2023), DOI: 1272,: 10.1016/j.molstruc.2022.134154

    • İlker Demirbolat; Necla Kulabas; Merve Gurboga; Ozlem Bingol ozakpinar; Gamze Çiftci;  Kemal Yelekci; Jianyang Liu; Per-Johan Jakobsson; Ozkan Danis; Ayse Ogan; Ilkay Küçükgüzel, “Synthesis and evaluation of antiproliferative and mPGES-1 inhibitory activities of novel carvacrol-triazole conjugates” ORGANIC COMMUNICATIONS (OCT-DEC 2022),  15 (4), p.  356-377. DOI: 10.25135/acg.oc.142.2212.2651

    • Yelekçi, K., Erdem, S.S. (2023). Computational Chemistry and Molecular Modeling of Reversible MAO Inhibitors. In: Binda, C. (eds) Monoamine Oxidase. Methods in Molecular Biology, vol 2558.  Springer Nature, Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2643-6_17.

    • Özkan Danış, Mohammad Musa Shirzad, Necla Kulabaş, Ömer Erdoğan, Özge Çevik, Damla Dere, Kemal Yelekçi, lkay Küçükgüzel, “Novel azole-urea hybrids as VEGFR-2 inhibitors: Synthesis, in vitro antiproliferative evaluation and in silico studies”, JOURNAL OF MOLECULAR STRUCTURE (2023), (Received minor revision).     
    • G. Akın Evingur, Önder Pekcan, Editors “Application and Characterization of Rubber Material” IntechOpen Limited, London, January, 2023).

    • Edited by G. Akın Evingur, Önder Pekcan “Elasticity of Materials” Intech Open Limited, London, May, 2023 .

2022

    • Celebi M.; Inan T.; Kurkcuoglu O.; Akten E. D. Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase. Chem. 2022, 280, 106701.

    doi: 10.1016/j.bpc.2021.106701  

    • Oguz, F. S.; Oguz, S. R.; Ogret, Y.; Karadeniz, T. S.; Senturk Ciftci, H.; Karatas, S.; Kivanc, D.; Aydin, F. Distribution of HLA epitope frequencies in Turkish population. Turkish J. of Biochemistry, 2022, 2022, 1-6.

    doi: 10.1515/tjb-2021-0083   

    • Celebi, M.; Akten, E. D. Altered Dynamics of S. Aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites. J. Mol. Biol. 2022, 167646.

    doi: 10.1016/J.JMB.2022.167646  

    • Polat, E. O.; Cetin, M. M.; Tabak, A. F.; Güven, E. B.; Uysal, B. Ö.; Arsan, T.; Kabbani, A.; Hamed, H.; Gül, S. B. Transducer Technologies for Biosensors and Their Wearable Applications. Biosens. 2022, 12(6), 385.

    doi: 10.3390/BIOS12060385

    • Özuğur Uysal, B.; Akın Evingür, G.; Pekcan, Ö. Polyacrylamide Mediated Polyvinyl Pyrrolidone Composites Incorporated with Aligned Molybdenum Disulfide. J. Appl. Polym. Sci. 2022, 139(18), 52061.

    doi: 10.1002/APP.52061

    doi: 10.1140/EPJS/S11734-022-00512-X

    • Braun, T.; Fernandez, C. N.; Eroglu, D.; Hartland, A.; Breitenbach, S. F. M.; Marwan, N. Sampling Rate-Corrected Analysis of Irregularly Sampled Time Series. Phys. Rev. E 2022, 105 (2), 024206.

    doi: 10.1103/PHYSREVE.105.024206/FIGURES/9/MEDIUM

    • Boumezber, S.; Yelekçi, K. Screening of Novel and Selective Inhibitors for Neuronal Nitric Oxide Synthase (NNOS) via Structure-Based Drug Design Techniques. J. Biomol. Struct. Dyn. 2022.

    doi: 10.1080/07391102.2022.2054471

    • Albayati, S.; Uba, A. I.; Yelekçi, K. Potential Inhibitors of Methionine Aminopeptidase Type II Identified via Structure-Based Pharmacophore Modeling. Mol. Divers. 2022, 26(2), 1005–1016.

    doi: 10.1007/S11030-021-10221-7/FIGURES/5

    • Birgül, K.; Uba, A. I.; Çuhadar, O.; Sevinç, S. K.; Tiryaki, S.; Tiber, P. M.; Orun, O.; Telci, D.; Yılmaz, Ö.; Yelekçi, K.; Güniz Küçükgüzel. Synthesis and Molecular Modeling of MetAP2 of Thiosemicarbazides, 1,2,4-Triazoles, Thioethers Derived from (S)-Naproxen as Possible Breast Cancer Agents. J. Mol. Struct. 2022, 1259.

    doi: 10.1016/J.MOLSTRUC.2022.132739

2021

  • Aksoy, H.; Şekerler, T.; Mert, N. M. In Silico Investigation of Wound Healing Potential of Some Compounds in Tubers of Asphodelus Species with GSK3-β Protein. Res. Pharm. 2021, 25(5) (25(5)), 740–747.

doi: 10.29228/jrp.65.

  • Al-Obaidi, A.; Elmezayen, A. D.; Yelekçi, K. Homology Modeling of Human GABA-AT and Devise Some Novel and Potent Inhibitors via Computer-Aided Drug Design Techniques. Biomol. Struct. Dyn. 2021, 39 (11), 4100–4110.

doi: 10.1080/07391102.2020.1774417.

  • Albayati, S.; Uba, A. I.; Yelekçi, K. Potential Inhibitors of Methionine Aminopeptidase Type II Identified via Structure-Based Pharmacophore Modeling. Divers. 2021.

doi: 10.1007/s11030-021-10221-7.

  • Arda, E.; Kara, S.; Pekcan, Ö.; Akın Evingür, G. Evaluation of the Fractal Dimension of Polyacrylamide during Gelation and Swelling. Today Commun. 2021, 26, 101980.

doi: 10.1016/j.mtcomm.2020.101980.

  • Banerjee, A.; Goswami, B.; Hirata, Y.; Eroglu, D.; Merz, B.; Kurths, J.; Marwan, N. Recurrence Analysis of Extreme Event-like Data. Nonlinear Process. Geophys. 2021, 28 (2), 213–229.

doi: 10.5194/npg-28-213-2021.

  • Beytur, S. Marker Residue Types at the Structural Regions of Transmembrane Alpha‐helical and Beta‐barrel Interfaces. Proteins Struct. Funct. Bioinforma. 2021, 89 (9), 1145–1157.

doi: 10.1002/prot.26087.

  • Dutta, K.; Elmezayen, A. D.; Al-Obaidi, A.; Zhu, W.; Morozova, O. V.; Shityakov, S.; Khalifa, I. Seq12, Seq12m, and Seq13m, Peptide Analogues of the Spike Glycoprotein Shows Antiviral Properties against SARS-CoV-2: An in Silico Study through Molecular Docking, Molecular Dynamics Simulation, and MM-PB/GBSA Calculations. Mol. Struct. 2021, 1246, 131113.

doi: 10.1016/j.molstruc.2021.131113.

  • Düzkan, B.; Uysal, B. Ö.; Pekcan, Ö. Surfactant-Free One-Step Fabrication of Gelatin/PAAm/MWCNT Composites for Biomedical Applications. Bull. 2021.

doi: 10.1007/s00289-021-03574-4.

  • Elmezayen, A. D.; Al-Obaidi, A.; Yelekçi, K. Discovery of Novel Isoform-Selective Histone Deacetylases 5 and 9 Inhibitors through Combined Ligand-Based Pharmacophore Modeling, Molecular Mocking, and Molecular Dynamics Simulations for Cancer Treatment. Mol. Graph. Model. 2021, 106, 107937.

doi: 10.1016/j.jmgm.2021.107937.

  • Elmezayen, A. D.; Al-Obaidi, A.; Şahin, A. T.; Yelekçi, K. Drug Repurposing for Coronavirus (COVID-19): In Silico Screening of Known Drugs against Coronavirus 3CL Hydrolase and Protease Enzymes. Biomol. Struct. Dyn. 2021, 39 (8), 2980–2992.

doi: 10.1080/07391102.2020.1758791.

  • Elmezayen, A. D.; Yelekçi, K. Structure-Based Virtual Screening for Novel Potential Selective Inhibitors of Class IIa Histone Deacetylases for Cancer Treatment. Biol. Chem. 2021, 92, 107491.

doi: 10.1016/j.compbiolchem.2021.107491.

  • Elmezayen, A. D.; Yelekçi, K. Homology Modeling and in Silico Design of Novel and Potential Dual-Acting Inhibitors of Human Histone Deacetylases HDAC5 and HDAC9 Isozymes. Biomol. Struct. Dyn. 2021, 39 (17), 6396–6414.

doi: 10.1080/07391102.2020.1798812.

  • Essiz, S.; Gencel, M.; Aktolun, M.; Demir, A.; Carpenter, T. S.; Servili, B. Correlated Conformational Dynamics of the Human GluN1-GluN2A Type N-Methyl-D-Aspartate (NMDA) Receptor. Mol. Model. 2021, 27 (6), 162.

doi: 10.1007/s00894-021-04755-8.

  • Evingür, G. A.; Sağlam, N. A.; Çimen, B.; Uysal, B. Ö.; Pekcan, Ö. The WS 2 Dependence on the Elasticity and Optical Band Gap Energies of Swollen PAAm Composites. Compos. Mater. 2021, 55 (1), 71–76.

doi: 10.1177/0021998320944210.

  • Hu, G.; Doruker, P.; Li, H.; Demet Akten, E. Editorial: Understanding Protein Dynamics, Binding and Allostery for Drug Design. Mol. Biosci. 2021, 8.

doi: 10.3389/fmolb.2021.681364.

  • Marwan, N.; Donges, J. F.; Donner, R. V.; Eroglu, D. Nonlinear Time Series Analysis of Palaeoclimate Proxy Records. Sci. Rev. 2021, 274, 107245.

doi: 10.1016/j.quascirev.2021.107245.

  • Metin, R.; Akten, E. D. Drug Repositioning to Propose Alternative Modulators for Glucocorticoid Receptor through Structure-Based Virtual Screening. Biomol. Struct. Dyn. 2021, 1–16.

doi: 10.1080/07391102.2021.1960608.

  • Nayır, Ş.; Kıvrak, S.; Kara, İ.; Uysal, B. Ö.; Pekcan, Ö. Tungsten Disulfide (WS2) Doped Polyacrylamide (PAAm) Composites: Gelation and Optical Studies. Optik (Stuttg). 2021, 245, 167673.

doi: 10.1016/j.ijleo.2021.167673.

  • Özuğur Uysal, B.; Akın Evingür, G.; Pekcan, Ö. Polyacrylamide Mediated Polyvinyl Pyrrolidone Composites Incorporated with Aligned Molybdenum Disulfide. Appl. Polym. Sci. 2021, 52061.

doi: 10.1002/app.52061.

  • Salgin-Goksen, U.; Telli, G.; Erikci, A.; Dedecengiz, E.; Tel, B. C.; Kaynak, F. B.; Yelekci, K.; Ucar, G.; Gokhan-Kelekci, N. New 2-Pyrazoline and Hydrazone Derivatives as Potent and Selective Monoamine Oxidase A Inhibitors. Med. Chem. 2021, 64 (4), 1989–2009.

doi: 10.1021/acs.jmedchem.0c01504.

  • Nayır, Ş.; Kıvrak, S.; Kara, İ.; Uysal, B. Ö.; Pekcan, Ö. Tungsten Disulfide (WS2) Doped Polyacrylamide (PAAm) Composites: Gelation and Optical Studies. Optik (Stuttg). 2021, 245, 167673.

doi: 10.1016/J.IJLEO.2021.167673

2020

    • Aksoy, H.; Şekerler, T.; Mert, N. M. In Silico Investigation of Wound Healing Potential of Some Compounds in Tubers of Asphodelus Species with GSK3-β Protein. Res. Pharm. 2021, 25(5) (25(5)), 740–747.

    doi: 10.29228/jrp.65.

    • Al-Obaidi, A.; Elmezayen, A. D.; Yelekçi, K. Homology Modeling of Human GABA-AT and Devise Some Novel and Potent Inhibitors via Computer-Aided Drug Design Techniques. Biomol. Struct. Dyn. 2021, 39 (11), 4100–4110.

    doi: 10.1080/07391102.2020.1774417.

    • Albayati, S.; Uba, A. I.; Yelekçi, K. Potential Inhibitors of Methionine Aminopeptidase Type II Identified via Structure-Based Pharmacophore Modeling. Divers. 2021.

    doi: 10.1007/s11030-021-10221-7.

    • Arda, E.; Kara, S.; Pekcan, Ö.; Akın Evingür, G. Evaluation of the Fractal Dimension of Polyacrylamide during Gelation and Swelling. Today Commun. 2021, 26, 101980.

    doi: 10.1016/j.mtcomm.2020.101980.

    • Banerjee, A.; Goswami, B.; Hirata, Y.; Eroglu, D.; Merz, B.; Kurths, J.; Marwan, N. Recurrence Analysis of Extreme Event-like Data. Nonlinear Process. Geophys. 2021, 28 (2), 213–229.

    doi: 10.5194/npg-28-213-2021.

    • Beytur, S. Marker Residue Types at the Structural Regions of Transmembrane Alpha‐helical and Beta‐barrel Interfaces. Proteins Struct. Funct. Bioinforma. 2021, 89 (9), 1145–1157.

    doi: 10.1002/prot.26087.

    • Dutta, K.; Elmezayen, A. D.; Al-Obaidi, A.; Zhu, W.; Morozova, O. V.; Shityakov, S.; Khalifa, I. Seq12, Seq12m, and Seq13m, Peptide Analogues of the Spike Glycoprotein Shows Antiviral Properties against SARS-CoV-2: An in Silico Study through Molecular Docking, Molecular Dynamics Simulation, and MM-PB/GBSA Calculations. Mol. Struct. 2021, 1246, 131113.

    doi: 10.1016/j.molstruc.2021.131113.

    • Düzkan, B.; Uysal, B. Ö.; Pekcan, Ö. Surfactant-Free One-Step Fabrication of Gelatin/PAAm/MWCNT Composites for Biomedical Applications. Bull. 2021.

    doi: 10.1007/s00289-021-03574-4.

    • Elmezayen, A. D.; Al-Obaidi, A.; Yelekçi, K. Discovery of Novel Isoform-Selective Histone Deacetylases 5 and 9 Inhibitors through Combined Ligand-Based Pharmacophore Modeling, Molecular Mocking, and Molecular Dynamics Simulations for Cancer Treatment. Mol. Graph. Model. 2021, 106, 107937.

    doi: 10.1016/j.jmgm.2021.107937.

    • Elmezayen, A. D.; Al-Obaidi, A.; Şahin, A. T.; Yelekçi, K. Drug Repurposing for Coronavirus (COVID-19): In Silico Screening of Known Drugs against Coronavirus 3CL Hydrolase and Protease Enzymes. Biomol. Struct. Dyn. 2021, 39 (8), 2980–2992.

    doi: 10.1080/07391102.2020.1758791.

    • Elmezayen, A. D.; Yelekçi, K. Structure-Based Virtual Screening for Novel Potential Selective Inhibitors of Class IIa Histone Deacetylases for Cancer Treatment. Biol. Chem. 2021, 92, 107491.

    doi: 10.1016/j.compbiolchem.2021.107491.

    • Elmezayen, A. D.; Yelekçi, K. Homology Modeling and in Silico Design of Novel and Potential Dual-Acting Inhibitors of Human Histone Deacetylases HDAC5 and HDAC9 Isozymes. Biomol. Struct. Dyn. 2021, 39 (17), 6396–6414.

    doi: 10.1080/07391102.2020.1798812.

    • Essiz, S.; Gencel, M.; Aktolun, M.; Demir, A.; Carpenter, T. S.; Servili, B. Correlated Conformational Dynamics of the Human GluN1-GluN2A Type N-Methyl-D-Aspartate (NMDA) Receptor. Mol. Model. 2021, 27 (6), 162.

    doi: 10.1007/s00894-021-04755-8.

    • Evingür, G. A.; Sağlam, N. A.; Çimen, B.; Uysal, B. Ö.; Pekcan, Ö. The WS 2 Dependence on the Elasticity and Optical Band Gap Energies of Swollen PAAm Composites. Compos. Mater. 2021, 55 (1), 71–76.

    doi: 10.1177/0021998320944210.

    • Hu, G.; Doruker, P.; Li, H.; Demet Akten, E. Editorial: Understanding Protein Dynamics, Binding and Allostery for Drug Design. Mol. Biosci. 2021, 8.

    doi: 10.3389/fmolb.2021.681364.

    • Marwan, N.; Donges, J. F.; Donner, R. V.; Eroglu, D. Nonlinear Time Series Analysis of Palaeoclimate Proxy Records. Sci. Rev. 2021, 274, 107245.

    doi: 10.1016/j.quascirev.2021.107245.

    • Metin, R.; Akten, E. D. Drug Repositioning to Propose Alternative Modulators for Glucocorticoid Receptor through Structure-Based Virtual Screening. Biomol. Struct. Dyn. 2021, 1–16.

    doi: 10.1080/07391102.2021.1960608.

    • Nayır, Ş.; Kıvrak, S.; Kara, İ.; Uysal, B. Ö.; Pekcan, Ö. Tungsten Disulfide (WS2) Doped Polyacrylamide (PAAm) Composites: Gelation and Optical Studies. Optik (Stuttg). 2021, 245, 167673.

    doi: 10.1016/j.ijleo.2021.167673.

    • Özuğur Uysal, B.; Akın Evingür, G.; Pekcan, Ö. Polyacrylamide Mediated Polyvinyl Pyrrolidone Composites Incorporated with Aligned Molybdenum Disulfide. Appl. Polym. Sci. 2021, 52061.

    doi: 10.1002/app.52061.

    • Salgin-Goksen, U.; Telli, G.; Erikci, A.; Dedecengiz, E.; Tel, B. C.; Kaynak, F. B.; Yelekci, K.; Ucar, G.; Gokhan-Kelekci, N. New 2-Pyrazoline and Hydrazone Derivatives as Potent and Selective Monoamine Oxidase A Inhibitors. Med. Chem. 2021, 64 (4), 1989–2009.

    doi: 10.1021/acs.jmedchem.0c01504.

    • Nayır, Ş.; Kıvrak, S.; Kara, İ.; Uysal, B. Ö.; Pekcan, Ö. Tungsten Disulfide (WS2) Doped Polyacrylamide (PAAm) Composites: Gelation and Optical Studies. Optik (Stuttg). 2021, 245, 167673.

    doi: 10.1016/J.IJLEO.2021.167673