Nurcan Tuncbag, PhD

Postdoctoral Associate
at Fraenkel Lab


Research Publications Webservers and Databases CV Biosketch

Office address:
Department of Biological Engineering
Massachusetts Institute of Technology
Building 16, Room 244
Cambridge, MA, 02139

E-mail: ntuncbag[at]mit[dot]edu

Research Interests

Systems biology of human glioblastoma
  • Combination of proteome, interactome and transcriptional data to infer sub-components of signaling and regulatory networks.
  • Revealing how the networks of interactions among proteins and genome are altered in cells during disease.
  • Simultenous re-construction of multiple pathways via prize-collecting Steiner forest.
Structural analysis and characterization of protein interactions using computational methods.
  • Construction of the non-redundant dataset of protein interfaces
  • Architectures and functional coverage of protein interfaces
  • Prediction of hot spots in protein interfaces
  • Prediction of protein-protein interactions using structural matching and flexible refinement
  • Incorporation of time dimensionality into protein interaction networks
  • Binding site cooperativity in multi-partner proteins

Publications

  • N.Tuncbag, S. Moskrin, S.C.Huang, E.Fraenkel, SteinerNet: A web server for integrating "omic" data to discover hidden components of response pathways Nucleic Acids Research (Web Server Issue), forthcoming

  • N.Tuncbag, A.Braunstein, A.Pagnani, S.C.Huang, J.Chayes, C.Borgs, R.Zecchina, E.Fraenkel, Simultaneous reconstruction of multiple signaling pathways via the prize-collecting Steiner forest problem, RECOMB Conference Proceeding, Barcelona/Spain

  • N.Tuncbag, O.Keskin, R.Nussinov, A.Gursoy, Fast and Accurate Modeling of Protein-Protein Interactions by Combining Template-Interface-Based Docking with Flexible Refinement, Proteins:Structure, Function and Bioinformatics, 2012, pubmed

  • N.Tuncbag, A.Gursoy, R.Nussinov, O.Keskin, Predicting Protein-Protein Interactions on a Proteome Scale by Matching Evolutionary and Structural Similarities at Interfaces Using PRISM, Nature Protocols, 2011, pubmed.
    Featured Protocol

  • N.Tuncbag, A.Gursoy, O.Keskin, Prediction of protein-protein interactions: Unifying evolution and structure at protein interfaces, Physical Biology, 2011, pubmed.

  • N.Tuncbag, O.Keskin, A.Gursoy, HotPoint:Hot spot prediction server for protein interfaces, Nucleic Acids Research, 2010, 38(Web Server issue):W402-6 pubmed.

  • N.Tuncbag, S.Salman, O.Keskin, A.Gursoy, Analysis and Network Representation of Hot Spots in Protein Interfaces Using Minimum Cut Trees, Proteins:Structure, Function & Bioinformatics, 2010, 78(10):2283-94. pubmed.

  • N. Tuncbag, G. Kar, A. Gursoy, O. Keskin, R. Nussinov, Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example, Molecular Biosystems, 2009, 5(12):1770-8. pubmed
    Amongst the top ten accessed articles in June and in July

  • N. Tuncbag, A. Gursoy, O. Keskin, Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy, Bioinformatics, 2009, 25(12):1513-20. pubmed
    "Fast Breaking Paper in Engineering" by Thomson Reuters and Science Watch in December 2010 in the field of Computer Science

  • N. Tuncbag, G. Kar, O. Keskin, A. Gursoy, R. Nussinov, A survey of available tools and web servers for analysis of protein - protein interactions and interfaces, Briefings in Bioinformatics, 2009, 10(3):217-32. pubmed

  • N. Tuncbag, E. Guney, R. Nussinov , A. Gursoy, O. Keskin. Architectures and Functional Coverage of Protein-Protein Interfaces, Journal of Molecular Biology Vol.:381, Issue:3, Pages:785-802, Sep, 2008. pubmed

  • O. Keskin, N. Tuncbag, A. Gursoy, Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks, Curr Pharmacet Biotech, Vol.:9, Issue:2, Pages:67-76, Apr, 2008. pubmed

  • E. Guney, N. Tuncbag, O. Keskin, A. Gursoy. HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6. pubmed

Conference Presentations and Posters

  • RECOMB 2012, Barcelona, Spain
    Travel Award, sponsored by ISCB.

  • ICBP Mathematical Modeling Meeting 2012, Tampa, USA

  • Protein Society Symposium 2011, Boston, USA.

  • Presented by Prof. Ruth Nussinov as Keynote, 3DSIG-ISMB/ECCB 2011, Vienna, Austria.

  • Biophysical Society Meeting 2011, Baltimore, USA

  • ISMB 2010, Boston, USA.

  • 3dSig-ISMB 2010, Boston, USA.

  • HIBIT'10, Antalya, Turkey

  • Computer Science Student Workshop (CSW'10), Istanbul, Turkey
    Best Work in-progress Paper Award

  • Tuncbag, N., Gursoy, A., Keskin O. Identification of Computational Hot Spots in Protein Interfaces Using Solvent Accessibility and Inter-Residue Potentials. Poster Presentation, ISMB/ECCB 2009, Stockholm, Sweden.
    Travel Fellowship, sponsored by BioSapiens

  • Tuncbag, N., Gursoy, A., Nussinov, R., Keskin O. Architectures and Functional Coverage of Protein-Protein Interfaces” Poster Presentation, 3dSig-ISMB/ECCB 2009, Stockholm, Sweden.

  • Guney E., Tuncbag, N., Keskin O., Gursoy, A. Large Scale Prediction of Hot Spots at Protein Interfaces. Poster Presentation, ECCB 2008, Cagliari, Italy.
    Travel Fellowship, sponsored by EMBRACE.

  • Tuncbag, N., Guney E., Ulubas, M.C., Keskin O., Gursoy, A. PRISM: A Web Server for Prediction and Visualization of Protein-Protein Interactions. Poster Presentation, ISMB/ECCB 2007, Vienna.
    Student Council Travel Award, sponsored by European Bioinformatics Institute (EBI).

  • Guney E., Tuncbag, N., Keskin O., Gursoy, A. HotSprint: Database of Computational Hot Spots at Protein Interfaces. Poster Presentation, ISMB/ECCB 2007, Vienna.

  • Tuncbag,N., Gursoy,A., Guney,E., Nussinov,R., Tsai,C.J., Keskin,O. A New Dataset of Protein-Protein Interfaces. 51st Biophysical Society Annual Meeting in Baltimore, Maryland, USA, March 3-7, 2007.

Webservers and Databases

(worked during Post-doctoral research period at MIT under supervision of Prof. Ernest Fraenkel at the Fraenkel Lab)

  • SteinerNet integrating "omic" data to discover hidden components of response pathways

(worked during PhD study at Koc University under supervision of Prof. Ozlem Keskin and Prof. Attila Gursoy at COSBI Lab)

  • PRISM Server - a method to predict protein-protein interactions and structural modeling of protein complexes
  • HotPoint server - an efficient method for calculation of computational hot spots in protein interfaces
  • PRINT Database - a database of protein-protein interfaces available in PDB