Yazar "RTEÜ, Mühendislik ve Mimarlık Fakültesi, Biyomühendislik Bölümü" için PubMed İndeksli Yayınlar Koleksiyonu listeleme
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The alpha-aurora kinases function in vascular development in arabidopsis
Lee, Kwang-Hee; Utku, Avcı; Qi, Liying; Wang, Huanzhong (Oxford Univ Press, 2019)The Aurora kinases are serine/threonine kinases with conserved functions in mitotic cell division in eukaryotes. in Arabidopsis, Aurora kinases play important roles in primary meristem maintenance, but their functions in ... -
Changes in the abundance of cell wall apiogalacturonan and xylogalacturonan and conservation of rhamnogalacturonan II structure during the diversification of the Lemnoideae
Avcı, Utku; Pena, Maria J.; O'Neill, Malcolm A. (Springer, 2018)Main conclusion the diversification of the Lemnoideae was accompanied by a reduction in the abundance of cell wall apiogalacturonan and an increase in xylogalacturonan whereas rhamnogalacturonan II structure and cross-linking ... -
Computational investigation of peptide binding stabilities of HLA-B*27 and HLA-B*44 alleles
Bunsuz, Asuman; Serçinoğlu, Onur; Özbek, Pemra (Elsevier Ltd, 2020)Major Histocompatibility Complex (MHC) is a cell surface glycoprotein that binds to foreign antigens and presents them to T lymphocyte cells on the surface of Antigen Presenting Cells (APCs) for appropriate immune recognition. ... -
Computational studies with flavonoids and terpenoids as BRPF1 inhibitors: in silico biological activity prediction, molecular docking, molecular dynamics simulations, MM/PBSA calculations
Yalçın Özkat, Gözde (Taylor & Francis Ltd., 2022)The BRPF1 protein is encoded by the BRPF1 gene. In addition, the BRPF1 gene is known to be upregulated in leukaemia. Recent studies have shown that it is also overexpressed in hepatocellular carcinoma (HCC) as well. ... -
Design, synthesis and biological evaluation of novel bischalcone derivatives as potential anticancer agents
Burmaoğlu, Serdar; Göbek, Arzu; Aydın, Büşra Öztürk; Yurtoğlu, Emine; Aydın, Büşra Nur; Yalçın Özkat, Gözde; Hepokur, Ceylan; Şimşek Özek, Nihal; Ayşin, Ferhunde; Altuntaş, Ramazan; Algül, Öztekin (Elsevier, 2021)Building on our previous work that discovered chalcone as a promising pharmacophore for anticancer activity, we have various other chalcone derivatives and have synthesized a series of novel bischalcone to explore their ... -
Design, synthesis, and computational studies of benzimidazole derivatives as new antitubercular agents
Yalçın Özkat, Gözde; Ersan, Ronak H.; Ülger, Mahmut; Ülger, Seda T.; Burmaoğlu, Serdar; Yıldız, İlkay; Algül, Öztekin (Taylor & Francis Ltd., 2022)The increase in the drug-resistant strains of Mycobacterium tuberculosis has led researchers to new drug targets. The development of new compounds that have effective inhibitory properties with the selective vital structure ... -
Desirable plant cell wall traits for higher-quality miscanthus lignocellulosic biomass
da Costa, Ricardo M. F.; Pattathil, Sivakumar; Avcı, Utku; Winters, Ana; Hahn, Michael G.; Bosch, Maurice (Bmc, 2019)Background: Lignocellulosic biomass from dedicated energy crops such as Miscanthus spp. is an important tool to combat anthropogenic climate change. However, we still do not exactly understand the sources of cell wall ... -
Determination of novel SARS-CoV-2 inhibitors by combination of machine learning and molecular modeling methods
Güner, Ersin; Özkan, Özgür; Yalçın Özkat, Gözde; Ölgen, Süreyya (Bentham Science, 2023)Introduction: Within the scope of the project, this study aimed to find novel inhibitors by combining computational methods. In order to design inhibitors, it was aimed to produce molecules similar to the RdRp inhibitor ... -
Discovery of 5-(or 6)-benzoxazoles and oxazolo[4,5-b]pyridines as novel candidate antitumor agents targeting hTopo II alpha
Karataş, Esin; Foto, Egemen; Ertan Bolelli, Tuğba; Yalçın Özkat, Gözde; Yılmaz, Serap; Ataei, Şanaz; Zilifdar, Fatma; Yıldız, İlkay (Elsevier, 2021)Discovery of novel anticancer drugs which have low toxicity and high activity is very significant area in anticancer drug research and development. One of the important targets for cancer treatment research is topoisomerase ... -
Identification of novel inhibitors of the ABC transporter BmrA
Serçinoğlu, Onur; Şentürk, Duygu; Altınışık Kaya, Fatma Ece; Avcı, Fatma Gizem; Frlan, Rok; Tomašič, Tihomir; Özbek, Pemra; Orelle, Cédric; Jault, Jean-Michel; Sarıyar Akbulut, Berna (Academic Press Inc., 2020)The resistance of microbes to commonly used antibiotics has become a worldwide health problem. A major underlying mechanism of microbial antibiotic resistance is the export of drugs from bacterial cells. Drug efflux is ... -
Molecular modeling strategies of cancer multidrug resistance
Yalçın Özkat, Gözde (Elsevier, 2021)Cancer remains a leading cause of morbidity and mortality worldwide. Hence, the increase in cancer cases observed in the elderly population, as well as in children and adolescents, makes human malignancies a prime target ... -
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism
Aydınkal, Rasim Murat; Serçinoğlu, Onur; Özbek, Pemra (Oxford Univ Press, 2019)ProSNEx (Protein Structure Network Explorer) is a web service for construction and analysis of Protein Structure Networks (PSNs) alongside amino acid flexibility, sequence conservation and annotation features. ProSNEx ... -
Sequence-structure-function relationships in class I MHC: A local frustration perspective
Serçinoğlu, Onur; Özbek, Pemra (Public Library Science, 2020)Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like ... -
Synthesis and molecular docking studies of some novel antimicrobial benzamides
Acar, Cemre; Yalçın Özkat, Gözde; Ertan-Bolelli, Tuğba; Onurdağ, Fatma Kaynak; Ökten, Suzan; Şener, Funda; Yıldız, İlkay (Academic Press Inc Elsevier Science, 2020)Common use of classical antibiotics has caused to the growing emergence of many resistant strains of pathogenic bacteria. Therefore, we aimed to synthesize a number of N-(2-hydroxy-(4 or 5)-nitrophenyl)benzamide derivatives ...