Visualizing the protein-protein interactions network in virtual reality and mixed reality environments

Şenderin, Büşra
Protein-protein interactions (PPI) define the physical contact of two or more protein structures. When these interactions are combined, the protein-protein interaction network (PPIN) is formed. The interactions between protein structures are distinct interactions—they happen in specific binding locations on proteins, and they have a specific biological function that they take on. With these networks, the processes within a cell or a living organism when healthy or diseased can be studied. In this thesis, a 3D visualization framework to envisage PPIs and PPINs in virtual reality (VR) and mixed reality (MR) environments will be developed. Detailed performance tests of the framework will be provided and analyzed for both VR and MR environments.


Parallelization of functional flow to predict protein functions
Akkoyun, Emrah; Can, Tolga; Department of Medical Informatics (2011)
Protein-protein interaction networks provide important information about what the biological function of proteins whose roles are unknown might be in a cell. These interaction networks were analyzed by a variety of approaches by running them on a single computer and the roles of the proteins identified were used to predict the function of the proteins unidentified. The functional flow is an approach that takes the network connectivity, distance effect, topology of the network with local and global views int...
Fast Screening of Protein-Protein Interactions Using Forster Resonance Energy Transfer (FRET-) Based Fluorescence Plate Reader Assay in Live Cells
Durhan, Seyda Tugce; Sezer, Enise Nalli; Son, Çağdaş Devrim; Küçük Baloğlu, Fatma (2022-11-01)
Protein-protein interactions (PPIs) have great importance for intracellular signal transduction and sustaining the homeostasis of an organism. Thus, the identification of PPIs is necessary to better understand the downstream signaling functions of the proteins in healthy and pathological conditions. Forster resonance energy transfer (FRET) between fluorescent proteins (FPs) is a powerful tool for detecting PPIs in living cells. In literature, FRET analysis methods such as donor photobleaching (FLIM), accept...
Modeling and simulation of metabolic networks for estimation of biomass accumulation parameters
Kaplan, U.; TÜRKAY, METİN; Biegler, L.; Karasözen, Bülent (2009-05-28)
Metabolic networks are defined as the collection of biochemical reactions within a cell that define the functions of that cell. Due to the growing need to understand the functions of biological organisms for industrial and medical purposes, modeling and simulation of metabolic networks has attracted a lot of attention recently. Traditionally, metabolic networks are modeled such as flux-balance analysis that considers the steady state nature of the cell. However, it is important to consider the dynamic behav...
GPCR-Gα protein precoupling: Interaction between Ste2p, a yeast GPCR, and Gpa1p, its Gα protein, is formed before ligand binding via the Ste2p C-terminal domain and the Gpa1p N-terminal domain
Cevheroğlu, Orkun; Becker, Jeffrey M.; Son, Çağdaş Devrim (Elsevier BV, 2017-12)
G protein coupled receptors bind ligands that initiate intracellular signaling cascades via heterotrimeric G proteins. In this study, involvement of the N-terminal residues of yeast G-alpha (Gpa1p) with the C-terminal residues of a full-length or C-terminally truncated Ste2p were investigated using bioluminescence resonance energy transfer (BRET), a non-radiative energy transfer phenomenon where protein-protein interactions can be quantified between a donor bioluminescent molecule and a suitable acceptor fl...
Integration of topological measures for eliminating non-specific interactions in protein interaction networks
BAYIR, Murat Ali; GUNEY, Tacettin Dogacan; Can, Tolga (Elsevier BV, 2009-05-28)
High-throughput protein interaction assays aim to provide a comprehensive list of interactions that govern the biological processes in a cell. These large-scale sets of interactions, represented as protein-protein interaction networks, are often analyzed by computational methods for detailed biological interpretation. However, as a result of the tradeoff between speed and accuracy, the interactions reported by high-throughput techniques occasionally include non-specific (i.e., false-positive) interactions. ...
Citation Formats
B. Şenderin, “Visualizing the protein-protein interactions network in virtual reality and mixed reality environments,” M.S. - Master of Science, Middle East Technical University, 2021.