Browsing M.S. Theses by Subject "Proteins."

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  • A computational approach for analysis of communication in proteins 
    Özel, Sinem. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2007., 2007.)
    Allostery and communication in proteins are crucial for the regulation of protein functions. The binding of a ligand changes the affinity of the protein at a distal ligand binding site and leads to conformational changes ...
  • A mechanistic view of cullin neddylation: allosteric conformational control of E3-ring ligases 
    Yıldırım, Melis. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.)
    Cullin-RING E3 ligases (CRLs), which constitute a superfamily of RING type E3 ligases, regulate ~20% of protein degradation by the ubiquitin-proteasome system in the cells. Cullin neddylation activates CRLs by urging a ...
  • A study on protein conformational transitions by Monte Carlo simulations 
    Aydın, Bahar. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.)
    Exploration of conformational transitions between two different conformational states of proteins reveals significant information about their action mechanism and function. In this thesis, the recently developed anisotropic ...
  • Hinge prediction using elastic network models 
    Emekli, Uğur. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2006., 2006.)
    The motion and interaction of rigid parts in a protein connected by hingers are important for the function of the protein. This makes identification of the hinge region particularly important. In this work a method and web ...
  • Investigation of dynamic allostery in motor proteins 
    Kaya, Cihan. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2013., 2013.)
    Allostery is a key concept in regulation of protein function. The communication pathways which are equivalent of the allosteric signaling or energy propagation pathways are the most significant aspect of allosteric mechanism. ...
  • Monte Carlo (MC) path generation and small-world network approach to identify functional residues in proteins 
    Armutlulu, Andaç. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)
    Allosteric mechanism of proteins is crucial for their proper functioning. An important aspect underlying this mechanism is the communication pathways connecting the regulatory and active sites of proteins. Monte Carlo (MC) ...
  • Structural dynamics of proteins in functional control 
    Özgüney, Rümeysa Büşra. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2020., 2020.)
    Manipulation of protein conformational ensembles are well-known phenomenon yielding the development of rational drug design strategies. As a novel contribution, the aim of this thesis is to mechanistically identify and ...
  • Study of protein-protein interfaces using Gaussian network model 
    Soner, Seren. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)
    The interface type of the proteins are useful in determining the functioning mechanism of proteins. The interface type may either be obligatory, non-obligatory or crystal (non biological). Previous studies have tried to ...

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