Characterization and prediction of protein interfaces to infer protein-protein interaction networks

Keskin, Ozlem
Tunçbağ, Nurcan
GÜRSOY, Attila
Complex protein-protein interaction networks govern biological processes in cells. Protein interfaces are the sites where proteins physically interact. Identification and characterization of protein interfaces will lead to understanding how proteins interact with each other and how they are involved in protein-protein interaction networks. What makes a given interface bind to different proteins; how similar/different the interactions in proteins are some key questions to be answered. Enormous amount of protein structures and experimental protein-protein interactions data necessitate advanced computational methods for analyzing and inferring new knowledge. Interface prediction methods use a wide range of sequence, structural and physico-chemical characteristics that distinguish interface residues from non-interface surface residues. Here, we present a review focusing on the characteristics of interfaces and the current status of interface prediction methods.


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Ozarar, M; Atalay, Mehmet Volkan; Atalay, Rengül (2004-04-30)
Subcellular localization is crucial for determining the functions of proteins. A system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order is designed. The approach for prediction is to find the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as featur...
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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. ...
Object-Oriented Segmentation of Cell Nuclei in Fluorescence Microscopy Images
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Cell nucleus segmentation remains an open and challenging problem especially to segment nuclei in cell clumps. Splitting a cell clump would be straightforward if the gradients of boundary pixels in-between the nuclei were always higher than the others. However, imperfections may exist: inhomogeneities of pixel intensities in a nucleus may cause to define spurious boundaries whereas insufficient pixel intensity differences at the border of overlapping nuclei may cause to miss some true boundary pixels. In co...
Live-cell imaging of Pol II promoter activity to monitor gene expression with RNA IMAGEtag reporters
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We describe a ribonucleic acid (RNA) reporter system for live-cell imaging of gene expression to detect changes in polymerase II activity on individual promoters in individual cells. The reporters use strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags) that can be expressed from a promoter of choice. For imaging, the cells are incubated with their ligands that are separately conjugated with one of the FRET pair, Cy3 and Cy5. The IMAGEtags were expressed in yeast from ...
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Tunçbağ, Nurcan; Keskin Özkaya, Zehra Özlem (null; 2006-08-25)
Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by ma...
Citation Formats
O. Keskin, N. Tunçbağ, and A. GÜRSOY, “Characterization and prediction of protein interfaces to infer protein-protein interaction networks,” CURRENT PHARMACEUTICAL BIOTECHNOLOGY, pp. 67–76, 2008, Accessed: 00, 2020. [Online]. Available: