Kurkcuoglu Levitas Lab


Research

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2022

Yuce M, Sarica Z, Ates B, Kurkcuoglu O (2022) Exploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow, Journal of Biomolecular Structure and Dynamics DOI:10.1080/07391102.2022.2051743 (Link)

Kocaaga B, FS Guner, Kurkcuoglu O (2022) Molecular dynamics simulations can predict the optimum drug loading amount in pectin hydrogels for controlled release, Materials Today Communications 31, 103268 (Link)

Kocaaga B, Kurkcuoglu O, Tatlier M, Dinler-Doganay G, Batirel S, Güner FS (2022) Pectin–Zeolite-Based Wound Dressings with Controlled Albumin Release, Polymers 14(3), 460 (Link)

Celebi M, Inan T, Kurkcuoglu O, Akten ED (2022) Potential Allosteric Sites Captured in Glycolytic Enzymes via Residue-Based Network Models: Phosphofructokinase, Glyceraldehyde-3-Phosphate Dehydrogenase and Pyruvate Kinase, Biophysical Chemistry 280, 106701 (Link).

2021

Ayvaz Koroglu M, Kurkcuoglu O, Sungur FA (2021) Monte Carlo and Molecular Dynamics Simulations Indicate Controlled Release of Corticosteroids from Mesoporous Host MIL-101 (Cr), Molecular Simulation, 47:18, 1530-1539 (Link).

Güzel P, Kürkçüoğlu Levitas Ö (2021) Kaba Ölçekli Elastik Ağyapı Modelleri ve Bakteriyel Ribozomun Yapı-İşlev İlişkisi, Protein: Yapısı, Mühendisliği, Etkileşimleri, Dinamiği ve İlaç Tasarımındaki Yeri, Ed. Saliha Ece Acuner, Ankara Nobel Tıp Yayınevi. (Book chapter) (Link)

Inan T, Dalgakiran D, Kurkcuoglu O, Güner FS (2021) Elucidating doxycycline loading and release performance of imprinted hydrogels with different cross-linker concentrations: A computational and experimental study, Journal of Polymer Research, 28:408, 1-19 (Link)

Yuce M, Cicek E, Inan T, Dag AB, Kurkcuoglu O, Sungur FA (2021) Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease, Proteins, 89(11):1425-1441.(Link)

Yeniyurt Y, Kilic S, Güner-Yılmaz ÖZ, Bozoglu S, Meran M, Baysak E, Kurkcuoglu O, Hizal G, Karatepe N, Batirel S, Güner FS (2021) Fmoc-PEG coated single-wall carbon nanotube carriers with non-covalent functionalization: an experimental and molecular dynamics study, Frontiers in Bioengineering and Biotechnology, 9: 648366. (Link)

Güner OZ, Kocaaga B, Batirel S, Kurkcuoglu O, Güner FS (2021) 2-Thiobarbituric acid addition improves structural integrity and controlled drug delivery of biocompatible pectin hydrogels, International Journal of Polymeric Materials and Polymeric Biomaterials, 70:10, 703-711 (Link)

Guvensoy-Morkoyun A, Kurkcuoglu O (2021) Computational assessment of thermostability in miRNA:CNT system using molecular dynamics simulations, Biochimica et Biophysica Acta (BBA) – General Subjects, 1865(2): 129808. (Link)

2020

Kurkcuoglu O, Gunes MU, Haliloglu T (2020) Local and Global Motions Underlying Antibiotic Binding in Bacterial Ribosome, Journal of Chemical Information and Modeling, 60, 12, 6447–6461. (Link)

Guzel P, Yildirim HZ, Yuce M, Kurkcuoglu O (2020) Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model, Frontiers in Molecular Biosciences, 7(586075) (Link)

2019

Akkus PD, Kurkcuoglu O (2019) Molecular dynamics simulations of adsorption of long pyrene-PEG chains on a thin carbon nanotube, Turkish Journal of Chemistry, 43: 1159-1169. (Link)

Kocaaga B, Kurkcuoglu O, Tatlier M, Batirel S, Güner FS (2019) Low-methoxyl pectin-zeolite hydrogels controlling drug release promote in vitro wound healing, Journal of Applied Polymer Science, 136, 47640. Doi: 10.1002/app.47640. (Most visited article in 2019) (Link)

2018

Eroglu B, Dalgakiran D, Inan T, Kurkcuoglu O, Güner FS (2018) A computational and experimental approach to develop minocycline-imprinted hydrogels and determination of their drug delivery performances, Journal of Polymer Research, 25: 258. (Link)

Erkal Ilhan S, Kürkçüoğlu Ö, Inan T, Güner ÖZ, Dalgakıran D, Okutan B, Torun Köse G, Kırmızı A, Okçu Heper A, Gürses Ö, Güner FS (2019) Preparation and Determination of In Vivo and In Vitro Performance of Doxycycline-Imprinted Contact Lenses for Corneal Neovascularization Treatment, Journal of the Turkish Chemical Society, 5(3): 1185-1192. (Link)

Meran M, Akkus PD, Kurkcuoglu O, Baysak E, Hizal G, Haciosmanoglu E, Unlu A, Karatepe N, Guner FS (2018), Non-covalent Pyrene-PEG Coatings of Carbon Nanotubes Achieve In Vitro Biocompatibility, Langmuir, 34(40), 12071-12082 doi: 10.1021/acs.langmuir.8b00971. (Link)

Kurkcuoglu O (2018) Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis, Turkish Journal of Biology, 42(5): 392-404. DOI: 10.3906/biy-1802-77. (Link)

Kurkcuoglu SS, Kurkcuoglu O, Güner FS (2018), A multiscale investigation on controlling bovine serum albumin adsorption onto polyurethane films, Journal of Applied Polymer Science, 45669, 1-14. (Link)

2017

Guzel P, Kurkcuoglu O (2017) Identification of potential allosteric communication pathways between functional sites of the bacterial ribosome by graph and elastic network models, Biochimica et Biophysica Acta (BBA) – General Subjects, 1861(12), 3131-3141 doi.org/10.1016/j.bbagen.2017.09.005 (Link)

Can MT, Kurkcuoglu Z, Ezeroglu G, Uyar A, Kurkcuoglu O, Doruker P (2017), Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states, PLoS ONE, 12(4): e0176262. (Link)

2004-2015

Kurkcuoglu O, Güner FS (2015), Polyurethane Surfaces: Protein Adsorption, Encyclopedia of Biomedical Polymers and Polymer Biomaterials, Mishra M Ed., Vol 9, pp. 6724-6742, Taylor & Francis, New York. (Book chapter) (Link)

Kurkcuoglu O, Doruker P (2013), Coarse-graining the nano-machine ribosome to elucidate its functional dynamics, Ribosomes: Molecular Structure, Role in Biological Functions and Implications for Genetic Diseases, Z. Lin and W. Liu Eds, pp 119-132, Nova Science Publishers, Inc. (Book chapter)(Link)

Uyar A, Kurkcuoglu O, Nilsson L, Doruker P (2011), The Elastic Network Model Reveals a Consistent Picture of Intrinsic Functional Dynamics of Type II Restriction Endonucleases, Pysical Biology, 8, 056001. (Link)

Kurkcuoglu O, Bates PA (2010), Mechanism of Cohesin Loading onto Chromosomes: A Conformational Dynamics Study, Biophysical Journal, 99(4), 1210-1220. (Link)

Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P (2009), Focused Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model, Biophysical Journal, 97(4), 1178-1187. (Link)

Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL (2009), Collective Dynamics of the Ribosomal Tunnel Revealed by Elastic Network Modeling, Proteins: Structure, Function and Bioinformatics, 75, 837-845. (Link)

Jernigan RL, Yang L, Song G, Kurkcuoglu O, Doruker P (2008), Elastic network models of coarse-grained proteins are effective for studying the structural control exerted over their dynamics, Coarse-Graining of Condensed Phase and Biomolecular Systems, ed. Gregory Voth, Taylor & Francis Group, LLC. (Book chapter)(Link)

Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL (2008), The Ribosome Structure Controls and Directs the mRNA Entry, Translocation and Exit Dynamics, Physical Biology, 5, 046005. (Cover article, Most visited article in Physical Biology in 2008)(Link)

Doruker P, Nilsson L, Kurkcuoglu O (2006), Collective Dynamics of EcoRI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations, Journal of Biomolecular Structure & Dynamics, 24(1), 1-15. (Cover article) (Link)

Kurkcuoglu O, Jernigan RL, Doruker P (2006), Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks, Biochemistry, 45, 1173-1182. (Link)

Kurkcuoglu O, Jernigan RL, Doruker P (2005), Collective Dynamics of Large Proteins from Mixed Coarse-Grained Elastic Network Model, QSAR & Combinatorial Science, 24, 443-448. (15th European Symposium on QSAR & Molecular Modeling, best poster award article) (Link)

Kurkcuoglu O, Jernigan RL, Doruker P (2004), Mixed Levels of Coarse-Graining of Large Proteins using Elastic Network Model Succeeds in Extracting the Slowest Motions, Polymer, 45, 649-657. (Link)