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Bioinformatics. 2007 Jun 15;23(12):1444-50. Epub 2007 Mar 24.

Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP).

Author information

1
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, PR China.

Abstract

MOTIVATION:

The rapid accumulation of single amino acid polymorphisms (SAPs), also known as non-synonymous single nucleotide polymorphisms (nsSNPs), brings the opportunities and needs to understand and predict their disease association. Currently published attributes are limited, the detailed mechanisms governing the disease association of a SAP remain unclear and thus, further investigation of new attributes and improvement of the prediction are desired.

RESULTS:

A SAP dataset was compiled from the Swiss-Prot variant pages. We extracted and demonstrated the effectiveness of several new biologically informative attributes including the structural neighbor profiles that describe the SAP's microenvironment, nearby functional sites that measure the structure-based and sequence-based distances between the SAP site and its nearby functional sites, aggregation properties that measure the likelihood of protein aggregation and disordered regions that consider whether the SAP is located in structurally disordered regions. The new attributes provided insights into the mechanisms of the disease association of SAPs. We built a support vector machines (SVMs) classifier employing a carefully selected set of new and previously published attributes. Through a strict protein-level 5-fold cross-validation, we attained an overall accuracy of 82.61%, and an MCC of 0.60. Moreover, a web server was developed to provide a user-friendly interface for biologists.

AVAILABILITY:

The web server is available at http://sapred.cbi.pku.edu.cn/

PMID:
17384424
DOI:
10.1093/bioinformatics/btm119
[Indexed for MEDLINE]

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