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Fragment-HMM: a new approach to protein structure prediction.

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.

SUBMITTER: Li SC 

PROVIDER: S-EPMC2578800 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature

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Fragment-HMM: a new approach to protein structure prediction.

Li Shuai Cheng SC   Bu Dongbo D   Xu Jinbo J   Li Ming M  

Protein science : a publication of the Protein Society 20080822 11

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  ...[more]

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