Search Results - "Kurkcuoglu, Zeynep"

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins by Kurkcuoglu, Zeynep, Doruker, Pemra

“…Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence…”
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ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution by Kurkcuoglu, Zeynep, Bahar, Ivet, Doruker, Pemra

“…Accurate sampling of conformational space and, in particular, the transitions between functional substates has been a challenge in molecular dynamic (MD)…”
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Correction: Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins by Kurkcuoglu, Zeynep, Doruker, Pemra

“…[This corrects the article DOI: 10.1371/journal.pone.0158063.]…”
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Coupling between catalytic loop motions and enzyme global dynamics by Kurkcuoglu, Zeynep, Bakan, Ahmet, Kocaman, Duygu, Bahar, Ivet, Doruker, Pemra

“…Catalytic loop motions facilitate substrate recognition and binding in many enzymes. While these motions appear to be highly flexible, their functional…”
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Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states by Can, Mehmet Tarik, Kurkcuoglu, Zeynep, Ezeroglu, Gokce, Uyar, Arzu, Kurkcuoglu, Ozge, Doruker, Pemra

“…The chaperone trigger factor (TF) binds to the ribosome exit tunnel and helps cotranslational folding of nascent chains (NC) in bacterial cells and…”
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An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45 by Koukos, Panagiotis I., Roel‐Touris, Jorge, Ambrosetti, Francesco, Geng, Cunliang, Schaarschmidt, Jörg, Trellet, Mikael E., Melquiond, Adrien S. J., Xue, Li C., Honorato, Rodrigo V., Moreira, Irina, Kurkcuoglu, Zeynep, Vangone, Anna, Bonvin, Alexandre M. J. J.

“…Our information‐driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part,…”
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Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase by Pemra Doruker, Zeynep Kurkcuoglu

“…The opening/closure of the catalytic loop 6 over the active site in apo triosephosphate isomerase (TIM) has been previously shown to be driven by the global…”
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Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human by Kurkcuoglu , Zeynep, Ural , Gulgun, Demet Akten, E., Doruker, Pemra

“…We aim to uncover the binding modes of benzothiazoles, which have been reported as specific inhibitors of triosephosphate isomerase from the parasite…”
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Anterior segment morphometry and intraocular pressure change after uneventful phacoemulsification by TAKMAZ, Tamer, KÖSEKAHYA, Pınar, KÜRKÇÜOĞLU, Piraye Zeynep

“…To evaluate the changes in anterior segment morphometry and intraocular pressure (IOP) with 3D rotating Scheimpflug camera-topography system after uneventful…”
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Choroidal Thickness in Patients with Systemic Lupus Erythematosus Analyzed by Spectral-domain Optical Coherence Tomography by Altinkaynak, Hasan, Duru, Necati, Uysal, Betül Seher, Erten, Şükran, Kürkcüoğlu, Piraye Zeynep, Yüksel, Nilay, Duru, Zeynep, Çağıl, Nurullah

“…Purpose: The aim of this study is to investigate the effect of systemic lupus erythematosus (SLE) on choroidal thickness (CT) in the subfoveal and perifoveal…”
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Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems by Kurkcuoglu, Zeynep, Bonvin, Alexandre M. J. J.

“…Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a challenge, especially when the extent and direction of the…”
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How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics by Kurkcuoglu, Zeynep, Findik, Doga, Akten, Ebru Demet, Doruker, Pemra

“…The tunnel region at triosephosphate isomerase (TIM)’s dimer interface, distant from its catalytic site, is a target site for certain benzothiazole derivatives…”
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Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 by Kurkcuoglu, Zeynep, Koukos, Panagiotis I., Citro, Nevia, Trellet, Mikael E., Rodrigues, J. P. G. L. M., Moreira, Irina S., Roel-Touris, Jorge, Melquiond, Adrien S. J., Geng, Cunliang, Schaarschmidt, Jörg, Xue, Li C., Vangone, Anna, Bonvin, A. M. J. J.

“…We present the performance of HADDOCK, our information-driven docking software, in the second edition of the D3R Grand Challenge. In this blind experiment,…”
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Understanding the Binding Specificity of G‑Protein Coupled Receptors toward G‑Proteins and Arrestins: Application to the Dopamine Receptor Family by Preto, A. J, Barreto, Carlos A. V, Baptista, Salete J, Almeida, José Guilherme de, Lemos, Agostinho, Melo, André, Cordeiro, M. Nátalia D. S, Kurkcuoglu, Zeynep, Melo, Rita, Moreira, Irina S

“…G-Protein coupled receptors (GPCRs) are involved in a myriad of pathways key for human physiology through the formation of complexes with intracellular…”
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Collective dynamics of the ribosomal tunnel revealed by elastic network modeling by Kurkcuoglu, Ozge, Kurkcuoglu, Zeynep, Doruker, Pemra, Jernigan, Robert L.

“…The collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode…”
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Full title: Collective Dynamics of the Ribosomal Tunnel Revealed by Elastic Network Modeling by Kurkcuoglu, Ozge, Kurkcuoglu, Zeynep, Doruker, Pemra, Jernigan, Robert L.

“…The collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode…”
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Blood coagulation parameters after intravitreal injection of aflibercept in patients with neovascular age-related macular degeneration by Altinkaynak, Hasan, Kars, Meltem Ece, Kurkcuoglu, Piraye Zeynep, Ugurlu, Nagihan

“…Purpose The aim of this study was to evaluate the effect of intravitreal injection of aflibercept (IVA) on blood coagulation tests in neovascular age-related…”
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A novel marker in acute central serous chorioretinopathy: thiol/disulfide homeostasis by Altinkaynak, Hasan, Kurkcuoglu, Piraye Zeynep, Caglayan, Mehtap, Yorgun, Mücella Arıkan, Yuksel, Nilay, Kosekahya, Pınar, Koca, Cemile, Toklu, Yasin

“…Purpose The aim of this study was to compare dynamic thiol/disulfide homeostatic status in acute central serous chorioretinopathy (CSCR) patients by using a…”
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INDIGO-DataCloud:A data and computing platform to facilitate seamless access to e-infrastructures by Collaboration, INDIGO-DataCloud, :, Salomoni, Davide, Campos, Isabel, Gaido, Luciano, de Lucas, Jesus Marco, Solagna, Peter, Gomes, Jorge, Matyska, Ludek, Fuhrman, Patrick, Hardt, Marcus, Donvito, Giacinto, Dutka, Lukasz, Plociennik, Marcin, Barbera, Roberto, Blanquer, Ignacio, Ceccanti, Andrea, David, Mario, Duma, Cristina, López-García, Alvaro, Moltó, Germán, Orviz, Pablo, Sustr, Zdenek, Viljoen, Matthew, Aguilar, Fernando, Alves, Luis, Antonacci, Marica, Antonelli, Lucio Angelo, Bagnasco, Stefano, Bonvin, Alexandre M. J. J, Bruno, Riccardo, Cetinic, Eva, Chen, Yin, Chiarello, Fabrizio, Costa, Alessandro, Pra, Stefano Dal, Davidovic, Davor, Dorigo, Alvise, Ertl, Benjamin, Fanzago, Federica, Fargetta, Marco, Fiore, Sandro, Gallozzi, Stefano, Kurkcuoglu, Zeynep, Lloret, Lara, Martins, Joao, Nuzzo, Alessandra, Nassisi, Paola, Palazzo, Cosimo, Pina, Joao, Sciacca, Eva, Segatta, Matteo, Sgaravatto, Massimo, Spiga, Daniele, Taneja, Sonia, Tangaro, Marco Antonio, Urbaniak, Michal, Vallero, Sara, Verlato, Marco, Wegh, Bas, Zaccolo, Valentina, Zambelli, Federico, Zangrando, Lisa, Zani, Stefano, Zok, Tomasz

“…This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud…”
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