Fragment-HMM: a new approach to protein structure prediction |
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Authors: | Li Shuai Cheng Bu Dongbo Xu Jinbo Li Ming |
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Affiliation: | David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L3G1, Canada. |
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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. |
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Keywords: | protein structure prediction hidden Markov model fragment assembly |
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