Browsing Araştırma Çıktıları | WoS | Scopus | TR-Dizin | PubMed by Author "Akten, Ebru Demet"
Now showing items 1-20 of 21
-
Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites
Celebi, Metehan; Akten, Ebru Demet (Academic Press Ltd- Elsevier Science Ltd, 2022)The effect of perturbation at the allosteric site was investigated through several replicas of molecular dynamics (MD) simulations conducted on bacterial phosphofructokinase (SaPFK). In our previous work, an alternative ... -
Assessing protein-ligand binding modes with computational tools: the case of PDE4B
Çifii, Gülşah; Aviyente, Viktorya; Akten, Ebru Demet; Monard, Gerald (Springer, 2017)In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects we present a protocol to rank newly designed molecules through the estimation of their IC values. Our ... -
Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human
Kurkcuoglu, Zeynep; Ural, Gulgun; Akten, Ebru Demet; Doruker, Pemra (Wiley-VCH Verlag GmbH, 2011)We aim to uncover the binding modes of benzothiazoles which have been reported as specific inhibitors of triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM) by performing blind dockings on both TcTIM and ... -
Classification Of Distinct Conformers Of Beta < 2-Adrenergic Receptor (Beta 2-AR) Based On Binding Affinity Of Ligands Through Docking Studies
Akten, Ebru Demet; Dilcan, Gonca (Amer Chemical Soc, 2016)B2AR reseptörü, akciğerlerin rahatlamasında ve kardiyovasküler fizyolojide rol oynamasıyla önemli bir ilaç hedefidir. Bu çalışmada, çeşitli B2AR konformasyonlarını aktif veya inaktif olarak sınıflandırmak amacıyla, ... -
Discovery of high affinity ligands for beta(2)-adrenergic receptor through pharmacophore-based high-throughput virtual screening and docking
Yakar, Rüya; Akten, Ebru Demet (Elsevier Science Inc, 2014)Novel high affinity compounds for human beta(2)-adrenergic receptor (beta(2)-AR) were searched among the clean drug-like subset of ZINC database consisting of 9928465 molecules that satisfy the Lipinski's rule of five. The ... -
Distinctive communication networks in inactive states of beta(2)-adrenergic receptor: Mutual information and entropy transfer analysis
Soğünmez, Nuray; Akten, Ebru Demet (Wiley, 2020)Mutual information and entropy transfer analysis employed on two inactive states of human beta-2 adrenergic receptor (beta(2)-AR) unraveled distinct communication pathways. Previously, a so-called "highly" inactive state ... -
A Docking Study Using Atomistic Conformers Generated via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex
Akten, Ebru Demet; Cansu, Sertan; Doruker, Pemra (Taylor & Francis Inc, 2009)Anisotropic network model is used to generate a set of distinct conformations for cylophilin A (CypA). The native structure is deformed to different extents along each of the lowest-frequency modes (first 7 modes) both in ... -
Docking-based virtual screening for potential activity against bacterial pyruvate kinase
Ergün, Çağla; Akten, Ebru Demet; Doruker, Pemra (Springer, 2017)[Abstract Not Available] -
Drug repositioning to propose alternative modulators for glucocorticoid receptor through structure-based virtual screening
Metin, Reyhan; Akten, Ebru Demet (Taylor & Francis Inc, 2022)Drug repositioning has recently become one of the widely used drug design approaches in proposing alternative compounds with potentially fewer side effects. In this study, structure-based pharmacophore modelling and docking ... -
Effect of intracellular loop 3 on intrinsic dynamics of human 2-adrenergic receptor
Ozcan, Ozer; Uyar, Arzu; Doruker, Pemra; Akten, Ebru Demet (Bmc, 2013)Background: To understand the effect of the long intracellular loop 3 (ICL3) on the intrinsic dynamics of human beta(2)-adrenergic receptor, molecular dynamics (MD) simulations were performed on two different models, both ... -
Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets
Ayyıldız, Merve; Çeliker, Serkan; Özhelvacı, Fatih; Akten, Ebru Demet (Frontiers Media, 2020)Three allosteric glycolytic enzymes, phosphofructokinase, glyceraldehyde-3 phosphate dehydrogenase and pyruvate kinase, associated with bacterial, parasitic and human species, were explored to identify potential allosteric ... -
Information Transfer in Active States of Human ?2-Adrenergic Receptor via Inter-Rotameric Motions of Loop Regions
Sogunmez, Nuray; Akten, Ebru Demet (Mdpi, 2022)Featured Application Loop regions in beta(2)AR are critical hot spot regions, likely in other GPCRs, and can be used as potential allosteric drug targets. Two independent 1.5 mu s long MD simulations were conducted for the ... -
Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human beta(2)-Adrenergic Receptor
Söğünmez, Nuray; Akten, Ebru Demet (Amer Chemical Soc, 2019)The alternative inactive state of the human beta(2)-adrenergic receptor originally exposed in molecular dynamics simulations was investigated using various analysis tools to evaluate causality between correlated residue-pair ... -
Investigation of allosteric communication pathways in human beta 2-adrenergic receptor
Akdaş, Başak; Kürkçüoğlu, Özge; Doruker, Pemra; Akten, Ebru Demet (Wiley-Blackwell, 2015)[Abstract Not Available] -
Investigation of Allosteric Coupling in Human Beta(2)-Adrenergic Receptor in the Presence of Intracellular Loop 3
Özgür, Canan; Doruker, Pemra; Akten, Ebru Demet (BMC, 2016)Background: This study investigates the allosteric coupling that exists between the intra- and extracellular parts of human beta(2)-adrenergic receptor (beta(2)-AR) in the presence of the intracellular loop 3 (ICL3) which ... -
Investigation of intrinsic dynamics and allosteric coupling in human beta 2-adrenergic receptor
Özcan, Özer; Özgür, Canan; Doruker, Pemra; Akten, Ebru Demet (Springer, 2017)[Abstract Not Available] -
Ligand-binding affinity of alternative conformers of human beta(2)-adrenergic receptor in the presence of intracellular loop 3 (ICL3) and their potential use in virtual screening studies
Dilcan, Gonca; Doruker, Pemra; Akten, Ebru Demet (Wiley, 2019)This study investigates the structural distinctiveness of orthosteric ligand-binding sites of several human beta(2) adrenergic receptor (beta(2)-AR) conformations that have been obtained from a set of independent molecular ... -
Molecular docking study based on pharmacophore modeling for novel PhosphodiesteraseIV ınhibitors
Cifci, Gulsah; Aviyente, Viktorya; Akten, Ebru Demet (Wiley-VCH Verlag GmbH, 2012)In this study pharmacophore modelling was carried out for novel PhosphodiesteraseIV (PDEIV) inhibitors. A pharmacophore-based virtual screening which resulted in 1959 hit compounds was performed with six chemical databases. ... -
Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase
Celebi, Metehan; Inan, Tugce; Kurkcuoglu, Ozge; Akten, Ebru Demet (Elsevier, 2022)Likelihood of new allosteric sites for glycolytic enzymes, phosphofructokinase (PFK), glyceraldehyde-3phosphate dehydrogenase (GADPH) and pyruvate kinase (PK) was evaluated for bacterial, parasitic and human species. ... -
Structural Analysis of Peptide Fragments Following The Hydrolysis of Bovine Serum Albumin by Trypsin and Chymotrypsin
Özyiğit, İbrahim Ethem; Akten, Ebru Demet; Pekcan, Önder (Taylor & Francis Inc, 2016)Peptide bond hydrolysis of bovine serum albumin (BSA) by chymotrypsin and trypsin was investigated by employing time-resolved fluorescence spectroscopy. As a fluorescent cross-linking reagent N-(1-pyrenyl) maleimide (PM) ...