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. 202125(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. 202139 (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. 202126, 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. 202128 (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. 202189 (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. 20211246, 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. 2021106, 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. 202139 (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. 202192, 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. 202139 (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. 202127 (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. 202155 (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. 20218.

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. 2021274, 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). 2021245, 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. 202164 (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

  • Atilgan, A.; Cetin, M. M.; Yu, J.; Beldjoudi, Y.; Liu, J.; Stern, C. L.; Cetin, F. M.; Islamoglu, T.; Farha, O. K.; Deria, P.; Stoddart, J. F.; Hupp, J. T. Post-Synthetically Elaborated BODIPY-Based Porous Organic Polymers (POPs) for the Photochemical Detoxification of a Sulfur Mustard Simulant. Am. Chem. Soc. 2020, 142 (43), 18554–18564.

doi: 10.1021/jacs.0c07784.

  • Ayyildiz, M.; Celiker, S.; Ozhelvaci, F.; Akten, E. D. Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets. Mol. Biosci. 2020, 7, 88.

doi: 10.3389/fmolb.2020.00088.

  • Birgül, K.; Yıldırım, Y.; Karasulu, H. Y.; Karasulu, E.; Uba, A. I.; Yelekçi, K.; Bekçi, H.; Cumaoğlu, A.; Kabasakal, L.; Yılmaz, Ö.; Küçükgüzel, Ş. G. Synthesis, Molecular Modeling, in Vivo Study and Anticancer Activity against Prostate Cancer of (+) (S)-Naproxen Derivatives. J. Med. Chem. 2020, 208, 112841.

doi: 10.1016/j.ejmech.2020.112841.

  • Ding, K.; Zhan, C.-G.; Elmezayen, A.; Yelekçi, K.; Erensoy, G. Synthesis, in Silico Studies and Cytotoxicity Evaluation of Novel 1,3,4-Oxadiazole Derivatives Designed as Potential MPGES-1 Inhibitors. Res. Pharm. 2020, 24 (4), 436–451.

doi: 10.35333/jrp.2020.187.

  • Eroğlu, D. Network Dynamics Reconstruction from Data. TURKISH J. Phys. 2020, 44 (4), 394–403.

doi: 10.3906/fiz-2004-7.

  • Eroglu, D.; Tanzi, M.; van Strien, S.; Pereira, T. Revealing Dynamics, Communities, and Criticality from Data. Rev. X 2020, 10 (2), 021047.

doi: 10.1103/PhysRevX.10.021047

  • Evingür, G. A.; Pekcan, Ö. Fractal Dimension and Phase Transition of Graphene Oxide (GO) Doped Polyacrylamide. Test. 2020, 84, 106386.

doi: 10.1016/j.polymertesting.2020.106386.

  • 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
  • Kucukdumlu, A.; Tuncbilek, M.; Guven, E. B.; Atalay, R. C. Design, Synthesis and In Vitro Cytotoxic Activity of New 6,9-Disubstituted Purine Analogues. Acta Chim. Slov. 2020, 67 (1), 70–82.

doi: 10.17344/acsi.2019.5196.

  • Prasad, S.; Marwan, N.; Eroglu, D.; Goswami, B.; Mishra, P. K.; Gaye, B.; Anoop, A.; Basavaiah, N.; Stebich, M.; Jehangir, A. Holocene Climate Forcings and Lacustrine Regime Shifts in the Indian Summer Monsoon Realm. Earth Surf. Process. Landforms 2020, 45 (15), 3842–3853.

doi: 10.1002/esp.5004.

  • Şahin, H. B.; Sayın, S.; Holder, M.; Buğra, K.; Çelik, A. Salt Inducible Kinases as Novel Notch Interactors in the Developing Drosophila Retina. PLoS One 2020, 15 (6), e0234744.

doi: 10.1371/journal.pone.0234744.

  • Sari, S.; Kart, D.; Öztürk, N.; Kaynak, F. B.; Gencel, M.; Taşkor, G.; Karakurt, A.; Saraç, S.; Eşsiz, Ş.; Dalkara, S. Corrigendum to “Discovery of New Azoles with Potent Activity against Candida Spp. and Candida Albicans Biofilms through Virtual Screening” [Eur. J. Med. Chem. 179 (2019) 634–648]. J. Med. Chem. 2020, 190 (11), 112130.

doi: 10.1016/j.ejmech.2020.112130.

  • Sogunmez, N.; Akten, E. D. Distinctive Communication Networks in Inactive States of β 2 ‐adrenergic Receptor: Mutual Information and Entropy Transfer Analysis. Proteins Struct. Funct. Bioinforma. 2020, 88 (11), 1458–1471.

doi: 10.1002/prot.25965.

  • Sunay, M. S.; Uğur, Ş.; Pekcan, Ö. Fluorescence and Photon Transmission Techniques for Studying Film Formation from PS/GO Nanocomposites. Bull. 2020, 77 (6), 3061–3077.

doi: 10.1007/s00289-019-02897-7.

  • Uba, A. I.; Yelekçi, K. Crystallographic Structure versus Homology Model: A Case Study of Molecular Dynamics Simulation of Human and Zebrafish Histone
  • Uysal, B. Ö.; Arier, Ü. Ö. A.; Pekcan, Ö. Tailoring the Electrical and Optical Properties of Carbon Nanotube Reinforced Transparent TiO2 Composites By Varying Nanotube Concentrations. Rev. Lett. 2020, 27 (02), 1950103.

doi: 10.1142/S0218625X19501038.

  • Weako, J.; Uba, A. I.; Keskin, Ö.; Gürsoy, A.; Yelekçi, K. Identification of Potential Inhibitors of Human Methionine Aminopeptidase (Type II) for Cancer Therapy: Structure-Based Virtual Screening, ADMET Prediction and Molecular Dynamics Studies. Biol. Chem. 2020, 86, 107244.

doi: 10.1016/j.compbiolchem.2020.107244.

  • Yılmaz, Ö.; Bayer, B.; Bekçi, H.; Uba, A. I.; Cumaoğlu, A.; Yelekçi, K.; Küçükgüzel, Ş. G. Synthesis, Anticancer Activity on Prostate Cancer Cell Lines and Molecular Modeling Studies of Flurbiprofen-Thioether Derivatives as Potential Target of MetAP (Type II). Chem. (Los. Angeles). 2020, 16 (6), 735–749.

doi: 10.2174/1573406415666190613162322.