Bo Hong received the Best Paper Award at the 2011 IEEE International Conference on Bioinformatics and Biomedicine, held November 12-15 in Atlanta.
An assistant professor in the School of Electrical and Computer Engineering (ECE) at Georgia Tech, Dr. Hong was honored for his paper, "Improving Prediction Accuracy of Protein-DNA Docking with GPU Computing." He shares this award with two coauthors–Jiadong Wu, his Ph.D. student, and Jun-tao Guo, a colleague from the Department of Bioinformatics and Biomedicine at the University of North Carolina at Charlotte.
Protein-DNA docking represents one of the most challenging problems in structural bioinformatics. Knowledge of how proteins interact with DNA is critical for understanding many key biological processes and for structure-based drug design. This paper describes a high performance computing method that Dr. Hong and his team have developed to tackle the protein-DNA docking problem using a GPU cluster. This protein-DNA docking algorithm integrates Monte-Carlo simulation and a simulated annealing method and has achieved 10.4 TFLOPS of sustained performance using 128 GPU cards, which represents 4× speed up over a traditional cluster with 1000 CPU cores. Such improved computation capability accelerates the conformational space sampling for the docking algorithm and increases the chance of finding near-native protein-DNA structures.