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Proteins. 2014 Apr;82(4):556-64. doi: 10.1002/prot.24421. Epub 2013 Oct 17.

SVR_CAF: an integrated score function for detecting native protein structures among decoys.

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  • 1Center for Systems Biology, Soochow University, Suzhou, Jiangsu, 215006, China.

Abstract

An accurate score function for detecting the most native-like models among a huge number of decoy sets is essential to the protein structure prediction. In this work, we developed a novel integrated score function (SVR_CAF) to discriminate native structures from decoys, as well as to rank near-native structures and select best decoys when native structures are absent. SVR_CAF is a machine learning score, which incorporates the contact energy based score (CE_score), amino acid network based score (AAN_score), and the fast Fourier transform based score (FFT_score). The score function was evaluated with four decoy sets for its discriminative ability and it shows higher overall performance than the state-of-the-art score functions.

Copyright © 2013 Wiley Periodicals, Inc.

KEYWORDS:

amino acid network; contact energy; fast Fourier transform; protein native structure selection; support vector regression

PMID:
24115148
[PubMed - indexed for MEDLINE]
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