2005年1月
Predicting absolute contact numbers of native protein structure from amino acid sequence
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- ,
- ,
- 巻
- 58
- 号
- 1
- 開始ページ
- 158
- 終了ページ
- 165
- 記述言語
- 英語
- 掲載種別
- DOI
- 10.1002/prot.20300
- 出版者・発行元
- WILEY-LISS
The contact number of an amino acid residue in a protein structure is defined by the number of C-beta atoms around the C-beta atom of the given residue, a quantity similar to, but different from, solvent accessible surface area. We present a method to predict the contact numbers of a protein from its amino acid sequence. The method is based on a simple linear regression scheme and predicts the absolute values of contact numbers. When single sequences are used for both parameter estimation and cross-validation, the present method predicts the contact numbers with a correlation coefficient of 0.555 on average. When multiple sequence alignments are used, the correlation increases to 0.627, which is a significant improvement over previous methods. In terms of discrete states prediction, the accuracies for 2-, 3-, and 10-state predictions are, respectively, 71.4%, 54.1%, and 18.9% with residue type-dependent unbiased thresholds, and 76.3%, 59.2%, and 21.8% with residue type-independent unbiased thresholds. The difference between accessible surface area and contact number from a prediction viewpoint and the application of contact number prediction to three-dimensional structure prediction are discussed. (C) 2004 Wiley-Liss, Inc.
- リンク情報
- ID情報
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- DOI : 10.1002/prot.20300
- ISSN : 0887-3585
- Web of Science ID : WOS:000225905000018