CAREER: A Structure-Based Approach to Transcription Factor-Binding Site Prediction via Protein-DNA Docking

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(This award is funded through the American Recovery and Reinvestment Act of 2009: Public Law 111-5).This is a CAREER award to support the research of Dr. Juntao Guo in the College of Computing and Informatics at the University of North Carolina - Charlotte. Dr. Guo is a second-year, tenure-track Assistant Professor. Advancing our knowledge of protein-DNA interaction mechanisms has implications for many aspects of biology including systems biology and evolution. Structure-based approaches will be used in the PI?s lab to investigate protein-DNA interactions, with a focus on gaining insight into the control of gene regulatory networks. This project is developing computational methods and the data and infrastructure resources required for genomic scale prediction of transcription factor (TF) binding sites by modeling protein-DNA interactions. A 3-dimensional structure of a transcription factor and a DNA sequence will be used to predict a protein-DNA complex model and the resulting binding model will then be used to predict the binding sites of the transcription factor. Results of this research will be a comprehensive protein-DNA complex structure database and benchmark sets for testing the results, algorithms for protein-DNA docking at two levels of resolution, structure-based methods for genome-scale TF-binding site prediction and a fully automated prediction server. The database and webserver will be available on the PI?s website: http://cciweb.uncc.edu/~jguo4/As a part of his CAREER plan, Dr. Guo will develop free publicly accessible infrastructure. Further, the PI is working closely with the Diversity in Information Technology Institute (DITI) and the STARS Alliance at UNC Charlotte to encourage participation of undergraduate students, especially those from underrepresented groups, in bioinformatics research. The PI will also play an active role in the Summer Institutes for Teaching Excellence (SITE) program offered by the Center for Mathematics, Science, and Technology Education (CMSTE) at UNC Charlotte to educate high school teachers. Finally, these research activities will be integrated into the bioinformatics education efforts in the newly established Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte.