Publications
[Google Scholar] [2016-2015] [2014-2012] [2011-2009] [2008-2004]
2016
Budeyri Gokgoz, N., Avci, F. G., Yoneten, K. K., Alaybeyoglu, B., Ozkirimli, E., Sayar, N. A., ... & Sariyar Akbulut, B. "Response of Escherichia coli to Prolonged Berberine Exposure." Microbial Drug Resistance. (2016).
Avci, F. G., Altinisik, F. E., Vardar Ulu, D., Ozkirimli Olmez, E., & Sariyar Akbulut, B. "An evolutionarily conserved allosteric site modulates beta-lactamase activity." Journal of Enzyme Inhibition and Medicinal Chemistry, 1-8. (2016).
Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür. "A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction." BMC bioinformatics 17.1 (2016): 1.
Deniz, Utku, Elif Ozkirimli, and Kutlu O. Ulgen. "A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors." Journal of Molecular Graphics and Modelling 63 (2016): 110-124.
2015
Alaybeyoglu, Begum, Berna Sariyar Akbulut, and Elif Ozkirimli. "Insights into Membrane Translocation of the Cell-Penetrating Peptide pVEC from Molecular Dynamics Calculations." Journal of Biomolecular Structure and Dynamics just-accepted (2015): 1-22.
Gökgöz, Nilay Büdeyri, et al. "Investigation of the in vivo interaction between β-lactamase and its inhibitor protein." Turkish Journal of Biology 39 (2015): 485-492.
Deniz, Utku, Kutlu O. Ulgen, and Elif Ozkirimli. "Identification of potential Tpx inhibitors against pathogen-host interactions." Computational Biology and Chemistry (2015).
Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür. "Classification of Beta-Lactamases and Penicillin Binding Proteins Using Ligand-Centric Network Models." PloS One 10.2 (2015): e0117874.
Alaybeyoglu, Begum, Berna Sariyar Akbulut, and Elif Ozkirimli. "A novel chimeric peptide with antimicrobial activity." Journal of Peptide Science (2015).
2014
Yilmaz, Oya Gursoy, Elif Ozkirimli Olmez, and Kutlu O. Ulgen. "Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening." Computational biology and chemistry 48 (2014): 1-13.
2013
Ozbuyukkaya, Gizem, Elif Ozkirimli Olmez, and Kutlu O. Ulgen. "Discovery of YopE Inhibitors by Pharmacophore-Based Virtual Screening and Docking." International Scholarly Research Notices 2013 (2013).
Gursoy, Oya, Elif Ozkirimli, and Kutlu O. Ulgen. "Identification of allosteric Akt inhibitors by computational methods." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. Vol. 246. 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC, 2013.
Alaybeyoglu, Begum, and Elif Ozkirimli. "Steered molecular dynamics provide insights into the translocation of the cell penetrating peptide pVEC." ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY. Vol. 246. 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC, 2013.
Özcan, Ahmet, Elif Ozkirimli Olmez, and Burak Alakent. "Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B." Proteins: Structure, Function, and Bioinformatics 81.5 (2013): 788-804.
Meneksedag, Deniz, et al. "Communication between the active site and the allosteric site in class A beta-lactamases." Computational biology and chemistry 43 (2013): 1-10.
Ozbuyukkaya, Gizem, Elif Ozkirimli Olmez, and Kutlu Ozergin Ulgen. "Aminopurine derivatives as putative SopE inhibitors." Journal of enzyme inhibition and medicinal chemistry 29.1 (2013): 137-145.
Ozkirimli, Elif. "The uptake mechanism of the cell-penetrating pVEC peptide." Journal of Chemistry 2013 (2013).
2012
Alaybeyoglu, Begum, Ihsan Omur Akdag, and Elif Ozkirimli Olmez. "Bacterial Uptake of the Cell-Penetrating Peptide pVEC." Biophysical Journal 102.3 (2012): 488a.
Meneksedag, Deniz, Asligul Dogan, and Elif Ozkirimli Olmez. "Communication Between an Allosteric Inhibitor Binding Site and the Active Site in Beta-Lactamase." Biophysical Journal 102.3 (2012): 463a.
Ulgen, Sefika Kutlu, Seval Aladag, and Elif Ozkirimli. "Virtual Screening and Docking of Potential Protein Kinase B Inhibitors." Biophysical Journal 102.3 (2012): 60a-61a.
Olmez, Elif Ozkirimli, and Berna Sariyar Akbulut. "Protein-peptide interactions revolutionize drug development." Binding Protein. Vol. 3. chapter, 2012.
2011
Olmez, E.O. and B. Alakent, Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B. Journal of Biomolecular Structure & Dynamics, 2011. 28(5): p. 675-693.
2010
Kanlikilicer, P., et al. Investigation of TEM-1 and SHV-1 beta-lactamase ligand binding. in Health Informatics and Bioinformatics (HIBIT), 2010 5th International Symposium on. 2010.
Budeyri, N., et al., In-vitro inhibitory effect of BLIP derived peptides on TEM-1 beta-lactamase. Febs Journal, 2010. 277: p. 108-108.
2009
Kanlikilicer, P., et al. Dynamic Analysis of beta Lactamase Ligand Interaction. in Biyomut: 2009 14th National Biomedical Engineering Meeting. 2009. İzmir.
Huang, H., E. Ozkirimli, and C.B. Post, Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions. Journal of Chemical Theory and Computation, 2009. 5(5): p. 1304-1314.
Gungormez, Y., E.O. Olmez, and K.O. Ulgen, Computational Prediction of Protein-Protein Interactions in Sphingolipid Signaling Network. Biyomut: 2009 14th National Biomedical Engineering Meeting, 2009: p. 231-234.
Budeyri, N., E.O. Olmez, and B.S. Akbulut, Investigation of in-vivo beta-lactamase inhibition by beta-lactamase-inhibitor-protein based peptides. Febs Journal, 2009. 276: p. 132-132.
Akkaya, A.E., et al., Investigation of blip - beta-lactamase binding in-vivo. Febs Journal, 2009. 276: p. 128-128.
2008
Ozkirimli, E., et al., An electrostatic network and long-range regulation of Src kinases. Protein Science, 2008. 17(11): p. 1871-1880.
2007
Oh, H., et al., Generation of an analog-sensitive syk tyrosine kinase for the study of signaling dynamics from the B cell antigen receptor. Journal of Biological Chemistry, 2007. 282(46): p. 33760-33768.
2006
Ozkirimli, E. and C.B. Post, Src kinase activation: A switched electrostatic network. Protein Science, 2006. 15(5): p. 1051-1062.
Ozkirimli, E. and C. Post, A switched electrostatic network guides Src conformational activation. Abstracts of Papers of the American Chemical Society, 2006. 231: p. 12-COMP.
2004
Ozkirimli, E. and C.B. Post, Pathway of Src-family tyrosine kinase activation and inactivation. Biophysical Journal, 2004. 86(1): p. 302A-303A.
