Posted February 15, 2012 Atlanta, GA
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.
About the School of Electrical and Computer Engineering
The School of Electrical and Computer Engineering (ECE) is one of eight schools and departments in the College of Engineering at the Georgia Institute of Technology. All ECE undergraduate and graduate programs are in the top 10 of the most recent college rankings by U.S. News & World Report. Over 2,500 students are enrolled in the School’s graduate and undergraduate programs, and in the last academic year, 723 degrees were awarded.
Over 110 ECE faculty members are involved in 11 areas of research, education, and commercialization – bioengineering, computer systems and software, digital signal processing, electric power, electromagnetics, electronic design and applications, microsystems, optics and photonics, systems and controls, telecommunications, and VLSI systems and digital design.
About the Georgia Institute of Technology
The Georgia Institute of Technology is one of the world's premier research universities. Ranked seventh among U.S. News & World Report's top public universities and the eighth best engineering and information technology university in the world by Shanghai Jiao Tong University's Academic Ranking of World Universities, Georgia Tech’s more than 20,000 students are enrolled in its Colleges of Architecture, Computing, Engineering, Liberal Arts, Business, and Sciences. Tech is among the nation's top producers of women and minority engineers. The Institute offers research opportunities to both undergraduate and graduate students and is home to more than 100 interdisciplinary units plus the Georgia Tech Research Institute.
