Bahar Akbal-Delibas

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Abstract. Developing applications for wireless sensor networks (WSN) is a complicated process because of the wide variety of WSN applications and lowlevel implementation details. Model-Driven Engineering offers an effective solution to WSN application developers by hiding the details of lower layers and raising the level of abstraction. However, balancing(More)
One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining(More)
Structural modeling of molecular assemblies lies at the heart of understanding molecular interactions and biological function. We present a method for docking protein molecules and elucidating native-like structures of protein dimers. Our method is based on geometric hashing to ensure the feasibility of searching the combined conformational space of dimeric(More)
Structural modeling of molecular assemblies promises to improve our understanding of molecular interactions and biological function. Even when focusing on modeling structures of protein dimers from knowledge of monomeric native structure, docking two rigid structures onto one another entails exploring a large configurational space. This paper presents a(More)
Detection of protein complexes and their structures is crucial for understanding their role in the basic biology of organisms. Computational docking methods can provide researchers with a good starting point for the analysis of protein complexes. However, these methods are often not accurate and their results need to be further refined to improve interface(More)
Detection of protein complexes and their structures is crucial for understanding the role of protein complexes in the basic biology of organisms. Computational methods can provide researchers with a good starting point for the analysis of protein complexes. However, computational docking methods are often not accurate and their results need to be further(More)
Protein-protein docking methods aim to compute the correct bound form of two or more proteins. One of the major challenges for docking methods is to accurately discriminate native-like structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic,(More)
We introduce a protein docking refinement method that accepts complexes consisting of any number of monomeric units. The method uses a scoring function based on a tight coupling between evolutionary conservation, geometry and physico-chemical interactions. Understanding the role of protein complexes in the basic biology of organisms heavily relies on the(More)
One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native(More)
In proteins, certain amino acids may play a critical role in determining their structure and function. Examples include flexible regions which allow domain motions, and highly conserved residues on functional interfaces which play a role in binding and interaction with other proteins. Detecting these regions facilitates the analysis and simulation of(More)