Computational Tools for Protein-DNA Interactions

Chris Kauffman and George Karypis
WIREs Data Mining and Knowledge Discovery, 2(1): 14-28, 2012
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Interactions between DNA and proteins are central to living systems, and characterizing how and when they occur would greatly enhance our understanding of working genomes. We review the different computational problems associated with protein-DNA interactions and the various methods used to solve them. A wide range of topics is covered including physics-based models for direct and indirect recognition, identification of transcription factor binding sites, and methods to predict DNA-binding proteins. Our goal is to introduce this important problem domain to data mining researchers by identifying the key issues and challenges inherent to the area as well as provide directions for fruitful future research.
Research topics: Bioinformatics | Cheminformatics