Browsing Ph.D. Theses by Author "Turgut, Pemra Doruker."

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Conformational transitions of proteins explored by Monte Carlo simulations integrated with collective modews

Çarşıbaşı, Nigar Kantarcı. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)

Elucidation of conformational transitions between open/closed or free/bound states of proteins sheds light on the mechanism of their action. In this thesis, a new technique (ANM-MC) is proposed, in which collective modes ...
Elastic network model based approaches for conformer generation and docking applications

Soner, Zeynep Kürkçuoğlu. (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.)

The dynamic nature of proteins poses challenging problems in computational biology, especially in terms of conformational sampling and transitions. In this thesis, an Elastic Network Model (ENM)-based computational method, ...
Mixed-resolution elastic network models for biological supramolecules

Levitas, Ayşe Özge Kürkçüoğlu. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)

Mixed coarse-graining approach has been recently introduced to the elastic network model to enable the modeling of a protein’s native conformation with regions of high- and low-resolution. In this model, each node of the ...

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