Zeynep Kurkcuoglu, PhD

Address: Utrecht, The Netherlands

E-mail: zeynepkurkcuoglu AT gmail DOT com

I am a chemical engineer, trained in computational modelling of biomolecular structures. During my PhD, I developed "ClustENM" to generate atomistic conformers for modelling the dynamics and flexibility of biomolecules of various sizes. Following the PhD, I worked as a postdoctoral researcher in Computational Structural Biology group in Utrecht University, focusing on modelling biomolecular complexes with an emphasis on flexibility, participating in community-wide challenges CAPRI, D3R Grand Challenge to predict protein-protein, protein-ligand complexes. I also worked in INDIGO-DataCloud project which aims at developing a data and computing platform targeting scientific communities. I gained extensive experience in molecular docking, molecular dynamics, computational modelling, data analysis and elastic networks. My skills in data cleaning, wrangling and analysis using various programming tools, lead me to become a data scientist. Currently, I apply statistical and machine learning techniques on health related data. I am always passionate about learning new skills and knowledge.

Work Experience

Data Scientist in NIPED Prevention BV11/2017-present

Hoorn, The Netherlands

- Statistical analysis, basic machine learning and data visualization in R, dynamic reporting in R Markdown

- Data preparation and delivery to collaborators, analysis for research questions

- Developed an R Shiny app for automated data check, analysis, visualization and dynamic reporting (.pptx format)

- Developed an R Shiny app for data visualization on Netherlands map

- Supervising intern for thesis project

- Benchmark compilation for comparative analysis using MongoDB, R

PostDoc in Computational Structural Biology Group09/2015-08/2017

Utrecht University, Department of Chemistry, Utrecht, The Netherlands

Supervisor: Prof. A.M.J.J. Bonvin

- Computational modelling of protein-ligand, protein-protein, protein-nucleic acids using homology modelling, docking, molecular dynamics and elastic networks (bash, C, Python, MATLAB)

- Participation as a team in community-wide challenges: CAPRI, D3R Grand Challenge

- "Champion" for We-NMR resarch community in INDIGO-DataCloud project which aims at developing a data and computing platform targeting scientific communities

- Testing INDIGO-DataCloud tools using Docker, VirtualBox on cloud platform, reporting in deliverables.

Teaching Assistant in Department of Chemical Engineering 12/2008-08/2015

Bogazici University, Istanbul, Turkey

- Assisting chemical engineering courses

- Coordinating Chemical Engineering Physicochemical Systems Laboratory course

Education

PhD, Chemical Engineering 07/2015

Bogazici University, Istanbul, Turkey. GPA: 4.00/4.00

Thesis title: "Elastic Network Model Based Approaches for Conformer Generation and Docking Applications"

Advisor: Prof. Pemra Doruker

MSc, Chemical Engineering 06/2009

Bogazici University, Istanbul, Turkey. GPA: 4.00/4.00

Advisor: Prof. Pemra Doruker

BSc, Chemical Engineering 06/2008

Bogazici University, Istanbul, Turkey. GPA: 3.79/4.00

Final project: “Structure-Based Drug Design on Triosephosphate Isomerase”

Lycee de Galatasaray, High School 06/2003

Istanbul, Turkey. GPA: 4.84/5.00

Academic/Teaching Experience

Teaching assistant 02/2016-04/2017

Department of Chemistry, Utrecht University, Utrecht, The Netherlands

  • NMR-spectroscopy & Molecular Modelling course

Teaching assistant 12/2008-08/2015

Department of Chemical Engineering, Bogazici University, Istanbul, Turkey

  • ChE 232 Chemical Engineering I: Fluid Mechanics
  • ChE 631 Transport Phenomena I
  • ChE 310 Introduction to Macromolecular Systems
  • ChE 413 Design and Simulations of Macromolecular Systems
  • ChE 516 Computational Biology and Bioinformatics
  • ChE 203 Physicochemical Systems Laboratory
  • ChE 302 Chemical Engineering Laboratory I
  • ChE 401 Chemical Engineering Laboratory II

Research assistant 09/2008-08/2015

Polymer Research Center, Bogazici University, Istanbul, Turkey

Visiting Scholar 07/2014-08/2014

Department of Computational and Systems Biology, University of Pittsburgh, School of Medicine, Pittsburgh, USA

Supervisor: Prof. Ivet Bahar

Project: “Assessment of elastic network model based hybrid techniques on conformational search”.

Coordinator of ChE 203 Physicochemical Systems Laboratory 2011-2015

Department of Chemical Engineering, Bogazici University, Istanbul, Turkey

Participated Projects

Researcher-"Champion" for Utrecht University-WeNMR in WP209/2015-08/2017

INtegrated Distributed data Infrastructures for Global ExplOitation (INDIGO)-Datacloud H2020 project

Use cases: HADDOCK Portal, PowerFit, DisVis

Researcher09/2014-08/2015

The Scientific and Technological Research Council of Turkey (TUBITAK) Project No. 113M237 “New computational methodologies on allosteric mechanisms and ligand binding”

Researcher 09/2009-08/2012

TUBITAK Project No. 109M213 "Development and application of hybrid algorithms for studying protein flexibility and conformational transitions"

Skills and Languages

Computer skills

  • Operating systems: Microsoft Windows, Unix-like OS
  • Programming: C, Python, R, bash, MATLAB
  • Software: PyMOL, VMD, UCSF Chimera, AMBER, NAMD, AutoDock, HADDOCK, Photoshop, Docker, Vagrant, Git, SPSS, Microsoft Office
  • Databases: SQL, MongoDB

Languages

  • Turkish, English, French
Scholarships, Awards, Memberships

Scholarships

  • TUBITAK Project No. 113M237, "New computational methodologies on allosteric mechanisms and ligand binding", 2014-2015.

  • National Scholarship Programme for PhD Students by TUBITAK, TUBITAK-BIDEB 2211, 09/2009 - 08/2013.

  • National Scholarship Programme for MSc Students by TUBITAK, TUBITAK-BIDEB 2210, 09/2008 - 08/2009.

Awards

  • Doctoral Dissemination Award for PhD Thesis “Elastic Network Model Based Approaches for Conformer Generation and Docking Applications”, Bogazici University, Istanbul, Turkey, 2016.

  • Wiley-VCH Prize 2011 for Best Poster Presentation for the poster named “’Ensemble’ docking studies of benzothiazoles to Trypanosoma cruzi and human triosephosphate isomerase”, VIII European Workshop in Drug Design, Certosa di Pontignano, Siena, Italy, 22-28 May 2011.

  • Bogazici University Chem. Eng. graduation awarded High Honors Certificate (3rd place) with GPA 3.79/4.00, 2008.

  • Lycee de Galatasaray graduation awarded in 3rd place with GPA 4.84/5.00, 2003.

Memberships

  • Biophysical Society, since 2010.
  • Bogazici University Alumni Association (BUMED), since 2008.
  • Galatasaray Alumni Association, since 2003.
  • Galatasaray Sports Club, since 2003
Publications
Participated Meetings and Workshops
  • 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”.

References
Available on request