Address: Utrecht, the Netherlands
I am a data scientist with a background in computational chemistry/biology and chemical engineering. Currently I work with health related data, develop tools for automated analysis, visualization and dynamic reporting using R, Python, Docker in Azure environment. I am always looking forward to develop my skills and knowledge.
Preto A.J., C.A.V Barreto, S. Baptista, J. Almeida, A.L.A. Melo, M.N.D.S. Cordeiro, Z. Kurkcuoglu, R. Melo, I.S. Moreira. Understanding the binding specificity of G-protein coupled receptors towards G-proteins and Arrestins: application to the dopamine receptor family. J. Chem. Inf. Model. 2020.
Koukos P.I., J. Roel-Touris, F. Ambrosetti, C. Geng, J. Schaarschmidt, M.E. Trellet, A.S.J. Melquiond, L.C. Xue, R.V. Honorato, I. Moreira, Z. Kurkcuoglu, A. Vangone, A.M.J.J. Bonvin. An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins: Struc. Funct. & Bioinformatics 2020, Advanced Online Publication.
Kurkcuoglu Z. & A.M.J.J. Bonvin. "Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems", Proteins 2019, 1– 15.
Koukos P.I., J. Roel-Touris, F. Ambrosetti, C. Geng, J. Schaarschmidt, M.E. Trellet, A.S.J. Melquiond, L.C. Xue, R.V. Honorato, I. Moreira, Z. Kurkcuoglu, A. Vangone & A.M.J.J. Bonvin. "An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45", BioRxiv 2019, 10.1101/718122v1.
Salomoni D., I. Campos, L. Gaido, J.M. de Lucas, P. Solagna, J. Gomes, L. Matyska, P. Fuhrman, M. Hardt, G. Donvito, L. Dutka, M. Plociennik, R. Barbera, I. Blanquer, A. Ceccanti, M. David, C. Duma, A. López-García, G. Moltó, P. Orviz, Z. Sustr, M. Viljoen, F. Aguilar, L. Alves, M. Antonacci, L.A. Antonelli, S. Bagnasco, A.M.J.J. Bonvin, R. Bruno, E. Cetinic, Y. Chen, A. Costa, D. Davidovic, B. Ertl, M. Fargetta, S. Fiore, S. Gallozzi, Z. Kurkcuoglu, L. Lloret, J. Martins, A. Nuzzo, P. Nassisi, C. Palazzo, J. Pina, E. Sciacca, D. Spiga, M.A. Tangaro, M. Urbaniak, S. Vallero, B. Wegh, V. Zaccolo, F. Zambelli, T. Zok. "INDIGO-DataCloud: A platform to facilitate seamless access to e-infrastructures", Journal of Grid Computing 2018, 16:381-408.
Bonvin A.M.J.J., C. Geng, M. van Dijk, E. Karaca, P. L. Kastritis, P.I. Koukos, Z. Kurkcuoglu, A.S.J. Melquiond, J.P.G.L.M. Rogrigues, J. Schaarschmidt, C. Schmitz, J. Roel-Touris, M.E. Trellet, S. de Vries, A. Vangone, L. Xue, G.C.P. van Zundert. "HADDOCK".In: Roberts G., Watts A., European Biophysical Societies (eds) Encyclopedia of Biophysics. Springer, Berlin, Heidelberg, 2018.
Kurkcuoglu Z.*, P.I. Koukos*, N. Citro, M.E. Trellet, J.P.G.L.M. Rodrigues, I.S. Moreira, J. Roel-Touris, A.S.J. Melquiond, C. Geng, J, Schaardschmidt, L.C. Xue, A. Vangone & A.M.J.J.Bonvin. “Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2”, Journal of Computer-Aided Molecular Design 2018, 32(1):175-185.
Can M.T., Z. Kurkcuoglu, G. Ezeroglu, A. Uyar, O. Kurkcuoglu & P. Doruker, "Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states", PLoS ONE 2017, 12(4): e0176262.
van Zundert G.C.P., M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato & A.M.J.J. Bonvin. "The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes", J. Mol. Biol. 2017, 429(3):399–407.
Vangone A., J.P.G.L.M. Rodrigues, L.C. Xue, G.C.P. van Zundert, C. Geng, Z. Kurkcuoglu, M. Nellen, S. Narasimhan, E. Karaca, M. van Dijk, A.S.J. Melquiond, K.M. Visscher, M. Trellet, P.L. Kastritis & A.M.J.J. Bonvin. "Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI Round 1", Proteins: Struc. Funct. & Bioinformatics 2017, 85: 417–423.
Trellet M., J. Schaarschmidt, G.C.P. van Zundert, Z. Kurkcuoglu, A.S.J. Melquiond & A.M.J.J. Bonvin. "Integrative modelling goes HPC/HTC", F1000Research 2016, 5:2216 (poster).
Kurkcuoglu Z. & A.M.J.J. Bonvin. "Science in the clouds: virtualizing HADDOCK, PowerFit and DisVis using INDIGO-DataCloud solutions", F1000Research 2016, 5:874 (poster).
Kurkcuoglu Z., I. Bahar & P. Doruker. “ClustENM: ENM-based sampling of essential conformational space at full atomic resolution”, Journal of Chemical Theory and Computation 2016, 12(9):4549-4562.
Kurkcuoglu Z. & P. Doruker. “Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins”, PLoS ONE 2016, 11(6): e0158063.
Kurkcuoglu Z., D. Findik, E.D. Akten & P. Doruker. “How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics”, Biophysical Journal 2015, 109(6):1169-1178.
Kurkcuoglu Z. & P. Doruker. “Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase”, Entropy 2013, 15(3):1085-1099.
Kurkcuoglu Z., A. Bakan, D. Kocaman, I. Bahar & P. Doruker. “Coupling between catalytic loop motions and enzyme global dynamics”, PLOS Computational Biology 2012, 8(9):e1002705.
Alakent B., Z. Kurkcuoglu & P. Doruker. “Functional dynamics of proteins elucidated by statistical analysis of simulation data”, Current Physical Chemistry 2012, 2(4):443-451.
Kurkcuoglu Z.*, G. Ural*, E.D. Akten & P. Doruker. “Blind dockings of benzothiazoles to multiple receptor conformations of triosephosphate isomerase from Trypanosoma cruzi and human”, Molecular Informatics 2011, 30:986-995.
Kurkcuoglu O., Z. Kurkcuoglu, P. Doruker & R.L. Jernigan. “Collective dynamics of the ribosomal tunnel revealed by elastic network modeling”, Proteins: Structure, Function, and Bioinformatics 2009, 75(4):837–845.
*Joint first author
ImmunAID goes big data, H2020 Course on Data Analysis, Erasmus MC, Rotterdam, the Netherlands, 25-26 June 2019.
Bioinformatics in Torun 2017, BIT17 Torun, Poland, 22-24 June 2017.
Invited speaker: “Integrative modelling of biomolecular complexes using HADDOCK”.
Workshop Instructor: “Protein-protein docking using HADDOCK”.
EGI Conference 2017 and INDIGO Summit 2017, Catania, Italy, 9-12 May 2017.
Oral presentation: “In transition towards Cloud: a use case in Structural Biology”.
Oral presentation: “DisVis and PowerFit: Explorative and Integrative Modeling of Biomolecular Complexes harvesting EGI GPGPU resources”.
2017 Bijvoet Symposium, Auditorium - Media Plaza, Jaarbeurs, Utrecht, the Netherlands, 10 April 2017.
Session Chair
Poster presentation: “Pre- and post-sampling conformational changes for protein-protein docking using elastic network modelling”.
7th Dutch Molecular Dynamics Day, Delft University of Technology, Delft, the Netherlands, 22 February 2017.
INDIGO-DataCloud All-Hands Meeting, Lisbon, Portugal, 6-9 February 2017.
CHAINS 2016 The Dutch Chemistry Conference, Veldhoven, the Netherlands, 7-8 December 2016.
Poster presentation: “Pre- and post-sampling conformational changes for protein-protein docking using elastic network modelling”.
EMBO Conference: Molecular Machines: Integrative Structural and Molecular Biology, Heidelberg, Germany, 20-23 November 2016.
Poster presentation: “Pre- and post-sampling conformational changes for protein-protein docking using elastic network modelling”.
Netherlands Society on Biomolecular Modelling fall meeting 2016, Utrecht, the Netherlands, 16 November 2016.
Poster presentation: “Pre- and post-sampling conformational changes for protein-protein docking using elastic network modelling”.
Digital Infrastructures for Research 2016, Krakow, Poland, 28-30 September 2016.
Poster presentation: “Science in the Clouds: Virtualization HADDOCK, PowerFit and DisVis using INDIGO-DataCloud Solutions”.
26th International BIOMOS Symposium on Biomolecular Simulation, Ausserberg, Switzerland, 14-16 September 2016.
INDIGO-DataCloud All-Hands Meeting, Laboratori Nazionali di Frascati, Frascati, Italy, 4-6 May 2016.
Short presentation: “Updates on Case Study in P4_1: HADDOCK, P4_2: DisVis, P4_3: PowerFit”.
2016 Bijvoet Symposium, Kontakt der Kontinenten, Soesterberg, the Netherlands, 25-26 April 2016.
Member of the jury for Poster Awards to PhD&MSc students
Poster presentation: “Science in the Clouds: Virtualizing HADDOCK, PowerFit and DisVis using INDIGO-DataCloud Solutions”.
6th Evaluation Meeting of the Critical Assessment of Protein Interactions (CAPRI 2016), Tel Aviv University, Tel Aviv, Israel, 17-19 April 2016.
Poster presentation: “Science in the Clouds: Virtualizing HADDOCK, PowerFit and DisVis using INDIGO-DataCloud Solutions”.
INDIGO Champions meet Developers, Amsterdam Science Park, Amsterdam, the Netherlands, 4-5 April 2016.
CHAINS 2015 The Dutch Chemistry Conference, Veldhoven, the Netherlands, 30 November-1 December 2015.
European Grid Infrastructure (EGI) Community Forum 2015, Bari, Italy, 10-13 November 2015.
AIMMS Post-Graduate Course: Practical Course in Biomolecular Modelling, Amsterdam, the Netherlands, 19-23 October 2015.
25th Intl. BIOMOS Symposium on Biomolecular Simulation, Ausserberg, Switzerland, 9-11 September 2015.
Oral presentation: “Inhibitor Effect on Triosephosphate Isomerase Dynamics: Local to Global Scale”.
ALGO SB Algorithms in Structural Bio-informatics winter school: Modeling Large Macromolecular Assemblies, Sophia Antipolis, France, 8-12 December 2014.
Poster presentation: “Generation of atomistic conformers using elastic network model for docking applications”.
Biophysical Society Thematic Meeting: Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey, 10-14 September 2014.
Poster presentation: “Generation of atomistic conformers using elastic network model for proteins undergoing large conformational changes and ribosome”.
Protein Folding Conference 2014, Grand Palladium Resort & Spa, Punta Cana, Dominican Republic, 16-19 July 2014.
Oral presentation: “Linking Enzyme Topology with Catalytic Loop Dynamics”.
2nd International BAU-Drug Design Symposium, Bahcesehir University, Istanbul, Turkey, 17-19 April 2014.
Poster presentation: “How an inhibitor bound to subunit interface alters receptor dynamics?”.
ALGO SB Algorithms in Structural Bio-informatics winter school: Modeling protein interactions, Sophia Antipolis, France, 2-7 December 2012.
Oral presentation: “Coupling between catalytic loop motions and enzyme dynamics: Triosephosphate isomerase case”.
Membrane Bound Protein & Ligand Docking Workshop, Sabanci University, Istanbul, Turkey, 19-21 September 2012.
Oral presentation: “Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human”.
CECAM Dynamics of Protein-Nucleic Acid Interactions: Integrating Simulations with Experiments, Zurich, Switzerland, 14-16 September 2011.
Poster presentation: “Generation of atomistic conformers using collective modes from elastic network model”.
Three-days HADDOCK workshop in Istanbul, Bogazici University, Istanbul, Turkey, 20-22 June 2011.
VIII European Workshop in Drug Design, Certosa di Pontignano, Siena, Italy, 22-28 May 2011.
Poster presentation: “’Ensemble’ docking studies of benzothiazoles to Trypanosoma cruzi and human triosephosphate isomerase”.
9th Chemical Physics Congress, Cesme, Izmir, Turkey, 14-16 October 2010.
Poster presentations: ”Ensemble docking studies of benzothiazoles to monomeric and dimeric triosephosphate isomerase”, “Conformational transition pathway of adenylate kinase using Monte Carlo simulations with collective modes”.
Biophysical Society 54th annual meeting, San Francisco, California, USA, 20-24 February 2010.
Poster presentation: “Docking study of benzothiazoles to triosephosphate isomerase including main chain flexibility”.
Summer School on Molecular Modeling and Drug Design, Istanbul, Turkey, 10-14 September 2008.
Poster presentation: “Effect of protein flexibility on the binding modes of benzothiazoles to TcTIM interface”.