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Browsing Boğaziçi Üniversitesi Tezleri by Subject "Proteins."

Browsing Boğaziçi Üniversitesi Tezleri 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 ...
  • Analysing drug taggets using ligand similarity 
    Öztürk, Hakime. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.)
    Analysis of the interactions between target proteins and drugs is crucial not only for drug discovery, but also for a better understanding of the possible evolutionary pressure that the drugs exert on the proteins. Based ...
  • Application of mixed coarse-grained elastic network model to protein-ligand interactions 
    Tezcan, Nurver. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2014., 2014.)
    Ligand binding to an active or allosteric regulatory site of enzyme may lead conformational changes or changes in protein dynamics. The aim of this thesis is to explore the effect of ligand binding on vibrational dynamics ...
  • Computational and experimental investigations into the mechanism of functional motion in biomolecular systems 
    Fas, Ayşe Burcu Aykaç. (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2016., 2016.)
    The seemingly random fluctuations that proteins exhibit in their native states actually harbor major contributions from the global/cooperative motions they undergo during functional transitions. Computationally efficient, ...
  • Effect of ligand binding on protein dynamics: a time series analysis 
    Başkan, Sena. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Internal dynamics of proteins can be analyzed by the help of simulation techniques, one of which is molecular dynamics (MD) simulation. Principal component analysis is commonly applied on large-sized MD simulation data to ...
  • Extracting protein-ligand interactions from the biomedical literature using deep learning approaches 
    Yüksel, Atakan. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.)
    Protein-ligand interactions play crucial roles in living organisms, thus they attract many researchers from various disciplines. There are protein-ligand interaction databases that provide information to researchers in a ...
  • Hardware acceleration for multiple sequence alignment of proteins 
    Ateşpare, İbrahim. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2019., 2019.)
    Multiple Sequence Alignment (MSA), which has been an active research area for a long time, is a computational task that is used in the field of bioinformatics. MSA for proteins involves the process of aligning three or more ...
  • 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) ...
  • Nonlinear oscillations of proteins 
    Demir, Veysi. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2006., 2006.)
    Slow modes of proteins exhibit nonlinear characteristics. Large deformations in proteins correspond to collective deformations. These are at relatively low energy compared to kBTroom where Troom is approximately 3000K. ...
  • Predicting intracellular functions of proteins from amino acid sequences using language processing methods 
    Çaldır, Bedirhan. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)
    Rapidly increasing computational power and sequencing technologies, which are at the peak of their development, enable the use of advanced algorithms with high processing volume to predict the intracellular functions of ...
  • 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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