Nikolaos Sgourakis' Home Page
  

Address:      Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polyechnic Institute, Troy NY 12180
Tel:            518-528-3385
E-mail:       sgournrpi.edu

Studies :

I graduated from the Biology department of the National University of Athens in 2004. I received my Master's degree in Bioinformatics from the same department in February 2006. Since the last year of my undergraduate studies I have been involved in research in Bioinformatics under the supervision of Professor Stavros Hamodrakas. In particular, I have focused on the development of tools that predict properties of G-protein coupled receptors (GPCRs), namely their interactions with G-proteins (coupling).
I am currently a PhD student of Biology at Rensselaer Polytechnic Institute, under the supervision of Professor Angel Garcia. Recent research involves the application of simulation tools for the characterization of of the conformational ensemble of the Alzheimer's peptides, and the correlated atomic motions of proteins. Our simulation results are validated through direct comparison with NMR data.
Another aspect of our research involves the simulation of membrane protein tertiary complexes.

Publications :

  • "Simulation of a protein tertiary complex: Study of the Interaction Interface and Conformational Dynamics of Dark State Rhodopsin in complex with Transducin"
    Sgourakis N.G and Garcia A.E. manuscript in preparation

  • "Helix Docking Dynamics: Interface Placticity and Conformational Dynamics Contributions to Molecular Recognition witihn a Ubiquitin/UIM Fusion Protein"
    Sgourakis N.G., Patel M., Garcia A.E., Makhatadze G.I. and McCallum S.A. manuscript in preparation

  • "Pressure effects on the ensemble dynamics of ubiquitin inspected with Molecular Dynamics simulations and isotropic Reorientational Eigenmode Dynamics"
    Sgourakis N.G., Day R., McCallum S.A. and Garcia A.E. Biophysical Journal 95:3943-3955 (2008);

  • "Computational Methods for the Prediction of GPCRs Coupling Selctivity"
    Sgourakis N.G., Bagos P.G. and Hamodrakas S.J. Handbook of Research for Systems Biology Applications in Medicine (Max Plank institute for Molecular Genetics, Berlin) 2008;

  • "Global versus local features of an unfolded peptide system - Abeta42 modeled by Replica Exchange Molecular Dynamics simulations and NMR experiments"
    Sgourakis N.G and Garcia A.E. Unfolded Proteins From Denatured to Intrinsically Disordered Trevor P. Creamer, Ed. Nova Science, Hauppauge, NY, 2008;

  • "The Alzheimer's Peptides Abeta40 and 42 Adopt Distinct Conformations in Water: A Combined MD / NMR Study"
    Sgourakis N.G., Yan Y., McCallum S.A., Wang C. and Garcia A.E. J. Mol. Biol. (2007) 368, 1448–1457;

  • "Prediction of the coupling specificity of GPCRs to four families of G-proteins using Hidden Markov Models and Artificial Neural Networks"
    Sgourakis N.G., Bagos P.G. and Hamodrakas S.J. Bioinformatics 2005 21(22):4101-4106;

  • "A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models"
    Sgourakis N.G., Bagos P.G., Papasaikas P.G. and Hamodrakas S.J. BMC Bioinformatics 2005 6:104;


    • full CV can be found here


    Awards and Honors :

  • NRW Undergraduate Science Award - 5/3/2007, Dusseldorf, Germany


    • Links :

  • Biophysics and Bioinformatics laboratory at the University of Athens

  • GPCR coupling prediction server

  • Center for Biotechnology and Interdisciplinary studies at RPI