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Seminar abstract


Fragment-HMM: A new approach to protein structure prediction

Dongbo Bu
Institute of Computing Technology, Chinese Academy of Sciences

Abstract :

We designed a simple position-specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly, clustering, target selection, refinement, and consensus, all in one process. Our initial implementation of this theory converges to within 6 A of the native structures for 100% of decoys on all six standard benchmark proteins used in ROSETTA (discussed by Simons and colleagues in a recent paper), which achieved only 14%–94% for the same data. The qualities of the best decoys and the final decoys our theory converges to are also notably better.


Dr. Bu received his Ph. D. degree from Institute of Computing Technology, Chinese Academy of Sciences in 2001. He did research in University of Waterloo, Canada as a post-doctoral fellow from 2006 to 2008. His research interests include algorithm design and analysis, including Satisfiability problem, Information Retrieval, and Bioinformatics.
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