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  A probabilistic model for secondary structure prediction from protein chemical shifts

Mechelke, M., & Habeck, M. (2013). A probabilistic model for secondary structure prediction from protein chemical shifts. Proteins: Structure, Function, and Bioinformatics, 81(6), 984-993. doi:10.1002/prot.24249.

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 Creators:
Mechelke, M1, Author           
Habeck, M1, Author           
Affiliations:
1Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3375791              

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 Abstract: Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts.

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Language(s): eng - English
 Dates: 2013-022013-06
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1002/prot.24249
PMID: 23292699
 Degree: -

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Title: Proteins: Structure, Function, and Bioinformatics
Source Genre: Journal
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Publ. Info: New York, NY : John Wiley & Sons
Pages: - Volume / Issue: 81 (6) Sequence Number: - Start / End Page: 984 - 993 Identifier: ISSN: 0887-3585
CoNE: https://pure.mpg.de/cone/journals/resource/954925553393_1